Because some players' motives and ambitions lie further than just being "part of a great system". None of us know Kroos personally so we wouldn't have a clue what he desires truly, but if he wants to be top dog at a club, he's got more chance at doing it at United where they are looking heavily to rebuild their midfield, rather than in an established one where he is fighting for spots with 3 or 4 brilliant midfielders. Some players thrive off being the main man, and in a team with the likes of Ribery, Robben and Schweinsteiger along with the emergence of the younger players in Muller, Thiago and Gotze, he may have far greater desire to be the CM of United for the next 5-10 years.
Secondly, the wages have been discussed as a key point: He has been in this Bayern squad for a few years now, yet they sign a player 3 years younger and give him double salaries. If you were in a job for 3 or 4 years, and the company hired a person younger than you for half the salary, would you smile at them and say " hey that's great news, don't worry about my salary going up or being similar, I'm fine just the way it is"? Like feck you would; you would want at least the same as him, considering these two are on the same level of talent at this stage for me, with Kroos being much better this season. Then you get United offering even more than what your club is offering, being the highest earner at the club (joint with Rooney) and one of the highest in the world? Yeah, what sort of monkey would do that.
He's not exactly a kid anymore, he's 24. To say he would need developing by a manager implies he isn't quite there at a top level yet, but the fact of the matter is that he is. He is one of the top CMs at 24, and even if this was his peak level then it's a bloody good peak to have still. On the contract part; isn't it a bit odd that they keep saying that the board will "try their best to keep hold of Toni" for almost 8 months now, since the summer transfer? Surely if he wanted to stay so bad, and they wanted to give him what he wants so bad, then they would have offered him a deal and he would have signed by now?
I'm not saying he will definitely sign for us, not by a long shot. But people being so adamant he won't sign because of the whole "Bayern and Pep are perfect" idea may be surprised if he does choose to leave, because some players' ambition run differently from one another.