"From the ground up" means all underlying tech. Examples:
- Our rendering engine started from a blank page of code, meaning that every single stadium, texture, helmet, piece of equipment, etc had to be re-authored.
- Our animation engine (i.e. tools & technology) was started from scratch with the objective of sharing among all EA Sports games. The tool & core technology was extremely early in development so Madden had MAJOR pains getting this up and running while having to re-add and tag every single animation in the game
- Models & skeletons were all re-created from scratch, so every single animation from current-gen had to either be re-captured, thrown out, or re-purposed (which is why you still see a few animations that made it over from PS2 days)
- We re-authored our entire UI system to not be a homebrew tool but rather a company wide solution - again, same thing as animation - lots of growing pains as we had to re-author every single screen in the game
- The entire game went from being written in normal C to C++, so nearly every line of code had to be refactored.
So those base level technologies all being re-written caused a major amount of work. When you talk about things not being radically different (I assume you mean gameplay because obviously graphics obviously are different), it's mainly because there was a ton of time that had to be spent to get ALL of those technologies up to an ultra-high quality, and in the meantime plenty of code had to be ported over or maybe re-worked a bit. As another example, I know I've seen you mention things like 'suction blocking' before - that's actually a totally different issue at it's core between the two animation engines, but to the consumer it may look the same. It's a problem of having enough variety in matching animations vs. the AI going to find those animations...but the way that problem manifests is 100% different between the two generations.
There is also a whole hidden layer to you guys of how your development tools support fast iteration time, and if your technologies don't create an easy-to-tune process it doesn't matter how good they are (since you can't make changes rapidly). This is something that we are REALLY seeing improve drastically across the board at Tiburon & EA as a whole and it's one of those things that really can separate good games from the bad.
As for your last question, I would likely not re-write the whole thing again...it'd be in chunks. We did have some major advantages of not being shackled (i.e. we really would just not have been able to do a lot of the things we do now in the old animation system), and I don't think there's any way we could move over to the shared animation tech (the ANT tool) at this point if we didn't do it back then, but that could have been selectively attacked instead of dropping EVERYTHING. It's just not acceptable to lose all your features AND start fresh with a whole new suite of gameplay and animation tech. And believe me even after all the pain of the 1st transition, I hope I'm the guy that gets to make the calls this time.
FIFA did a damn good approach on the transition - they added a secondary R&D team to work and rebuild their animation & gameplay engine for FIFA 07, while putting their core team on figuring out rendering and stuff for 06. I think this was probably better than the 2k approach of basically just up-rezzing, but now I look at NBA 2k7, 2k8, 2k9 and see that you still can obviously make a great game by doing that approach. The trade-off I think is that you keep your depth but you might be more limited graphically or maybe with future growth (just speculating on that).