A compare-and-contrast discussion topic? Time to write an essay!
So, on storyline attention, it looks like this comes down to four teams: The Toa Mata/Nuva, The Metru/Hordika, the Inika/Mahri, and the Okotan Masters/Uniters. Lots of other Toa teams existed in G1, sure, but none were released as sets in full or had all their characters fleshed out and featured as Toa, so when we're talking about story, four it is. For sets, I'd prefer to judge the waves individually, though, regardless of set lineage. Apart from the early Mata/Nuva, I think the differences between the sets were sufficiently great to allow that.
'01 & '03 Mata/Nuva: The Toa Mata/Nuva will definitely have a big nostalgia factor for a lot of people (particularly their Mata forms where I'm concerned), but objectively their sets were at best middling compared to either what came later or what was released with them. First off, they have garbage for articulation; in particular, the lack of any joint in the neck really hurts their expression in posing. Barring that, though, they had pretty good functions (arm flailing is still the gold standard), and their vibrant color schemes and expressive masks really helped to drive home the characters they represented.
'08 Nuva: The '08 adaptive armor versions did a lot better in the posability department, but threw away most of what looked good and defined the characters in the earlier sets and paled in comparison to their Makuta adversaries to boot. Their silver and gray-centered color schemes were at best bland, and most of their masks looked either outright bizarre or at least didn't evoke much of who they were before. Nynrah ghost blasters were alright as blasters go, but really, couldn't Gali and Onua have had at least one secondary weapon? Also, holy fragile sockets, Batman!
Metru: The Metru brought a much greater amount of articulation to the party and were some of the best proportioned humanoid sets that Bionicle ever released. They also retained the arm-swinging function in the package, though the lack of a ball joint in or near the shoulder area meant that it kind of hampered their posability even more than that of the Nuva; maybe it's just me, but for good-looking action poses shoulder articulation is a lot more useful than working elbows. The Metru's dour color schemes worked for their environment, but looking at them today, they really are horrifically bland. Good-looking masks, though...
Hordika: The Hordika are, in my opinion, actually an interesting experiment in building Toa mutants, and they definitely pulled that off, though with lots of gaps in their torsos that hampered their appearance. Shoulder posability returned, which was great, but the single-arm function felt a bit... lackluster compared to swinging the entire arm. Having the best of both worlds never really happened in G1. Points to the Hordika for having the rhotuka spinners, though; I had hours of fun with those, which is more than I could say for later launchers. Their mutated masks and weapons were pretty cool, too, but unfortunately only Vakama and Nuju made any effort to return any semblance of color to the sets beyond the addition of silver. Silver which, by the way, actually looked okay when used in modest quantities.
Inika: The Inika, of course, said 'screw it' when it came to built-in functions of any kind, opting instead for the launcher-only approach. Their build was new and novel at the time, and they were far more colorful than the Metru or Hordika before them, which is a plus. Light-up weapons were cool, too, though the same cannot be said for weird-looking proprietary masks and heads. Posability was awesome, but underneath the fancy new parts the sets were still clones.
Mahri: The Mahri took the Inika build philosophy, but brought back the normal masks and finally, finally dropped the clone set approach. Yes, they shared the same basic structure (if not necessarily the pieces), but unlike any other Toa before them, each Toa Mahri could actually be considered a relatively unique set, differentiated from its counterparts by more than just its mask, weapons, and color. Speaking of color; unique, vibrant, and more contrasting color schemes were tried on some of the Mahri as well, with only Kongu really suffering from the Metru palette. The Cordak blaster was cool looking, but too big and heavy for many of the sets and unreliable for some. Brittle joints started to become a factor as well, much to the disdain of MOCists everywhere.
Masters: Say what you will about CCBS, but with it and some technic the Masters managed to have the full range of posability of the old Inika build AND complete functions; no compromise except for some minor gripes about open ball joints and/or wacky proportions, and even those were not shared across all the sets. Some did have slightly larger flaws (Lewa's restricted head movement, for example), but nothing that all of them shared. Vibrant colors were present again, too, along with some really good mask designs.
Uniters:I'll give the Uniters points for ambition in their designs, what with the combining ability and all, but I've made no secret in the past of the fact that, across the board, I believe them to be inferior to the Masters. Their gear function, while unique, has made their proportions universally worse, their preference for two-handed weapons reduces posability, and some of them seem to be pulling the '08 trick of picking metallic primary colors. At least they've stayed away from gray, and some of them really do look good with their creatures, but on their own merit there are few Uniters that I feel can hold a candle to their previous iterations.
Therefore, set-wise, I believe the Masters to be the best of the lot. No other group of Toa sets ever came close to combining form and function so perfectly. Subjectively, though... I'd actually vote for the Mahri, though only by the slimmest of margins. You see, most of the fun I have with my sets comes from posing them, so even the best integrated function doesn't hold my interest for long unless it's a ridiculously clever build and/or allows the set to do something that actually looks... effective. Even the Masters' well executed arm-flailing is, in the end, still just arm-flailing, as far as I'm concerned. So, throwing the function out of the equation, it comes down to looks... and with a dose of nostalgia, the Mahri just have it for me. Make no mistake; I love the Masters as display sets, but the Mahri really had a widely varied aesthetic of their own down.
Mata/Nuva: no group of characters in either of Bionicle's runs were as burdened by destiny as this lot... and few squabbled as much among themselves (the Piraka take the prize, but still...). Really, though, the entirety of '01-'08 began and ended with the Toa Nuva, and one of them still featured prominently enough two years later to be released as a Star, not that such a release did any of the characters honored with it any real favors. Of course, I can't be entirely objective, given the extent to which I've delved into the personalities of these Toa on my own time, but they are and always will be Bionicle's original heroes, and a prime example of people with vastly different personalities and traits having to work together to accomplish one overarching goal. And, by and large, they succeeded, though not without setbacks, most notably their disastrous visit to Voya Nui.
Metru/Hordika: Who knew that '01's old Turaga had been Toa themselves? Cue two years of flashback! While '05 is often and in my opinion rightfully regarded as a weird shoe-in of a storyline, the Toa Hordika did actually pose some interesting questions that I wished Bionicle would've delved into deeper. Also, Vakama betraying the group is, well, iffy. However, big-time stuff went down in '04, and this team was the only one of which we got to see the entire journey from Matoran to Toa to Turaga, with quite a lot of character development along the way. While they never had quite the same feeling of destiny, great victory, or ('05 excepted) internal strife to them as their set-wise predecessors, I think the Metru were at least as significant story-wise.
Inika/Mahri: This team struck me always as the Toa that were never meant to be, or rather, circumstances necessitated drastic action on the part of whatever was running the Red Star to make sure Mata Nui's entire mission didn't go kaput with him... So, our intrepid Matoran from the days of MNOG were told to suit up to go save their heroes, and then their God. Tall order, that's for sure, and with it came the maturing, or as it's often described, darkening of the Bionicle story, which allowed the now Toa Inika and later Mahri to explore both the trials and tribulations of becoming a Toa and the concepts of leadership, morality, and ultimately sacrifice in far deeper and more meaningful ways than ever before. True, they (quite literally) didn't get the same amount of 'screentime' as the teams that had preceded them, but over the course of two years, they did deliver what I'd consider to be Bionicle's most powerful moments.
Master/Uniters: err... where to begin? We're now coming up on two years of G2, and only now is there actually a half-decent volume of story to talk about. So far, though, the Master's deliberately simple story and frequently cartoonish depictions has done them no real favors in making their journey seem... significant, I guess. The exact license that first the Hordika and then the Inika/Mahri were able to take in telling a more mature story is what's missing here so far, and hence, while they are great sets, I just don't really feel very invested in the Masters as characters, or in the struggles they have to overcome. That said, there is still time...
So... story-wise? This one is much more difficult to judge objectively, apart from the fact that, as it stands right now, the Masters clearly come last. All three flagship teams of G1 have a lot going for them; the Mata/Nuva started, drove, and concluded the story, the Metru/Hordika showed us the full life cycle of the Toa, and the Mahri delivered the feels... That said, the Toa Nuva actually adopted a lot of the themes the Mahri explored throughout '08; the sacrifice of the Toa Ignika, while less powerful than Matoro's, was significant, and Gali's Nova Blast in Karzahni had the makings of a powerful moment in its own right. So, on overall story impact... I think the Mata/Nuva do have it, both objectively and subjectively. Really, though, I think all the G1 teams won something by presenting a far more deeper and more mature story than pretty much any other Lego line had done up until that point.
Okay, I think I'm done now...