For me it was just the very wasted potential, on a worse scale than G2 even.
At least in G2 there was groundwork for the future. Things we deepening and picking up towards the end of the second year. It just didn't have time to develop.
Hero Factory, on the other hand, went on for what, 4-5 years? It had a really nice premise (that tied extremely well into the buildable figures theme), and there were a few interesting plot threads, but nothing was ever well explored. Everything moved too quickly for it to really get into the meat of things.
For what it was worth, the first television series was really good, though maybe a little light on world building (we got names of certain cities and places and such, but nothing substantial enough for me to say I'm familiar with even a place like Makuhero City). But it's still very enjoyable and laid the groundwork for an expanding galaxy.
Things escalated from there a bit, Trial by Fire felt more like a quick exposition to account for the new building system than anything else, but Savage Planet and Breakout were definitely the highlights of the series. Estranged HF employees, mysterious energy sources, a secret plot to overtake the HF from within, a secret Hero Recon Team, all very cool stuff to deviate from the status quo.
But everything afterward felt like a waste. Brain Attack had a secret villain orchestrating everything. Did we ever find out who that was or why he was doing it? Never. And then Invasion from Below might as well not exist. There is no story or personality to anything there. And to make matters worse, the characters and world from Breakout onward completely dropped all sense of continuity.
There was no Stormer/Furno rivalry or any furthering of their mentor/student relationship, Furno suddenly came into his own as a member of Alpha Squad after a point, Surge's supposed "flaw" was never explored in the slightest, Nex and Evo might as well have been interchangeable (they even changed Nex's entire personality between arcs), no tension because Hero Core depletion was dropped after Trial by Fire.
It's all such a shame really, because you can sort of tell they had much deeper things planned for the line. I myself can't help but imagine the story might have lead to something like Mr. Makuro dies or is killed and the Hero Factory gets overtaken and maybe becomes a "Villain Factory". Imagine a post-apocalyptic HF where only Alpha Team and a few scattered Heroes remain to have to fight off waves of mass-produced villains, all while their Hero Cores are slowly depleting without a Quaza Chamber to recharge them. What if some of the Heroes we came to know and love were killed off because their cores died, or some had to resort to crazy measures to keep themselves up? What if some Heroes had gone rogue in the collapse, pushing the status quo of the series of a clear divide between good and bad.
All amazing stuff. It's a shame the original vision never came to be, and it's also kind of a shame the line we did get never had the chance to go anywhere.