You have to plan EVERYTHING about a 3.5e character from 1-20, so I don't find that argument particularly convincing ...
Granted, it would be nice if it weren't quite so necessary to plan everything out, but that'll probably be necessary to some degree no matter what ...
I've never played a character that dipped, unfortunately, so I haven't experienced the problem personally. I have played a Swordsage/Mo9, and while I did have to plan my maneuvers and what I replaced when, it wasn't really any worse than planning out a Sorceror. I'm also in the process of rebuilding my wife's current character from full Knight to Knight 4/Crusader 9, and it won't really hurt any worse there, since the Crusader levels are all at the end. But I can see how dipping only a couple levels in the middle somewhere could be more difficult to figure out. Particularly if you're trying to cherry pick amongst a lot of disciplines, rather than focusing on a particular one.
Honestly, I don't think it's that big a burden. Yeah, it prevents you from cherry picking the very best maneuvers for every maneuver slot when you're dipping, but then, that provides an incentive to use the Martial Adept classes more heavily, since you'll get more slots AND have more chances to use the replacement mechanism. My SS wasn't even super optimized (I'd completely missed the unarmed adaptation, so I'd blown some feats on unarmed goodies that I wouldn't have had to otherwise, and I probably could've dipped a level or two in the other MA classes to get my prereqs for Mo9 more easily) and he was easily one of the more powerful characters in the group.
In a way, if you think about it, being able to cherry pick the very best spells (DM willing, anyway) is part of the reason the full casters kick so much ass. Only part, of course, since there's plenty of lower level kick ass spells too. But if you had to focus a little more to get the goodies rather than just going "Ding! Hello caster level 17! Bring on the universe-altering-goodness!", it might mitigate (a little) the metric asston of awesomeness that is the full core caster ...
Of course, as Hallack points out, it probably wouldn't add THAT much power to the initiators if you removed the "needs x maneuvers from this discipline" prereq, particularly since maneuvers aren't as powerful as spells of the same level. But I still lean a bit towards leaving it in there. I'm not MARRIED to it, so I'd certainly take advantage of that house rule if a DM presented it to me though ...
The restriction that I really DID chafe at when making my SS/Mo9 was the bit about replacing maneuvers. Technically, you can't do that when you're in a prestige class unless the prestige class says so. I would've LOVED being able to continue using the SS's replacement mechanic while taking Mo9 levels though.