Well, in a more literal sense, I feel that the Porkyman Company could have waited a bit to make Pokemon Racial Relations and its quickly rushed sequel to take the time to invest some actual development into the sequels, the alleged greatest of the past generation of consoles.
And I feel more time could have been invested into the development of the Wii-U instead of the hashery of mixed concepts but yet more of the same they presented, a la Professor Farnsworth as 'Their latest invention'. So much more technology could have been invested, as could have more attention to third parties.
Well, hard to say. I wish Need for Speed: Carbon had a lot more development time. It came out before the car industry started to push all of their biggest cars in games and were coming out with new stuff (Chevy started working on the Camero and Audi had a concept of the R8 as well as plenty of other companies who mainly found themselves with pretuned cars in the collector's edition of the game.) While the physics engine was okay at best, graphics wasn't worth mentioning, and the storyline didn't really do much service, the gameplay was actually pretty solid. Canyon races that were boss fights were actually fun, the idea of having to take over territory by winning races in sections was good at showing progress and avoid some repitition by having the races focused in certain areas that are designed for different kinds of cars, grouping cars up by general driving style actually made the game a bit easier to play for starters while not interfering with veterans, and the crew members were actually helpful and not a bunch of idiots. If I could, I would go back in time a recommend that the game be given an extra year or two in development (it seriously did not get a lot) with a difficulty setting (too hard for new people to the racing genre, too easy for people who play a lot of racing games,) a lot more content so as to add at least six more levels (only had 4, so six new bosses before the final area that are ever so increasing in size would add a lot to the single player mode with more areas and having every team challenge your areas to either get back in power or else teams trying to undermine you,) with push to get more concept cars from the auto industry and add them as modifiable cars, fixing of the Corvette and Audi R8 being too powerful, using punk buster or some software to prevent cheating online, and... well, can't think of anything beyond that.
Psychonauts or Grim Fandango. While Psychonauts would eventually gain more popularity and see rereleases on pretty much every downloadable site, Grim Fandango still remains nearly unplayable on modern systems (which is a shame, because I like it a little better and want more people to give it a go).
Uprising. It's a rts/shooter that didn't catch on, except for Battlezone and Urban Assault. It's an excellent game though.
EVO: Search for Eden. Basically Spore, if Spore was good.
Shin Megami Tensei: Pokemon, before Pokemon existed. Not certain if it did the monster battle first in general. It features alignments, contracts, and fusions. It wasn't until Persona that made the series popular.
Knuckles Chaotix: First Sonic game to do the team physics. It felt like an innovative take on the Sonic gameplay. My third fave from the Sonic franchise.