A few important things to note.
1) Longer battles are most fair when using the Tome of Battle in play. A martial adept is most effective, like a psionic character, when he or she can lay into the enemy with their best attacks for 1-4 rounds in a row (or just 1-2 rounds). If they have to stick around longer than that to fight, they'll have to use their less-effective maneuvers or start wasting turns on refreshing maneuvers (unless they're a Crusader, in which case they just gotta start the random cycle of maneuver-granting over again, given their wierd maneuver use and recovery mechanics). Throw more mooks at the party, or just tougher (not harder-hitting, but more survivable) enemies, to draw out the battles a bit longer.
So in a longer battle, core characters will be able to show their strengths better, rather than being outdone by the martial adept who used up his best attacks in the first 1-2 rounds (just like a psionic manifester who blows power points on a fully-augmented blasting power in the first few rounds and then has to be miserly to avoid running out of juice).
Similarly, martial adepts are best at melee combat, especially with just one or two enemies at a time. So wizards and druids and such can show their awesomeness at blowing up lots of stuff at once if you throw more mooks into the battle. Using ranged combatants also helps prevent martial adepts from outshining other folks; so as long as you don't skew the battles toward them by using all-melee fights, with just a few enemies at a time (which is just the normal tendency for some DMs), you shouldn't have problems with martial adepts. Each class has its strengths, and a martial adept's is 'melee dueling'.
2) Part of the balancing factor, I think, for Bo9S classes is that they're all kind of dependant on multiple ability scores. Crusaders usually need good Constitution and Charisma, but they also need Strength for offense. Swordsages need everything except Charisma, though they have only a minor need for Intelligence (and Strength, if using the Shadow Blade feat alongside Weapon Finesse). Warblades need Strength and Dexterity, and also at least reasonably good Constitution, along with Intelligence if they want to make the most of their class features.
3) Each martial adept class has its own advantages, and it's debatable which of them is strongest. However I'm generally inclined to believe that Swordsages are the most balanced when compared to core classes; a bit stronger from their versatility compared to Fighters, but then, Fighters are the weakest of the core warrior-types (usually; and this is less true when you use a lot of splatbooks that give nice feats to Fighters).
Crusaders are probably the strongest, but they also have tricky, kind of complicated mechanics, so if a player can handle one well, they deserve to be reasonably strong given the difficulty of running them. Mostly Crusaders are just tough, though, so it's not like they're offensive powerhouses.
Warblades may be the strongest or the weakest, people debate it all the time it seems. They're advantage compared to Fighters is lessened by the fact that they need more class levels before they can take any Fighter-specific feat.
4) A few maneuvers should be houseruled or just banned for simplicity. These include Swooping Dragon Strike, Warmaster's Charge, White Raven Tactics, and I think one of the high-level White Raven maneuvers besides those (I forget the name). Just generally watch out for White Raven maneuvers/stances, they're not all bad but many of them are very potent/efficient compared to other maneuvers/stances. You may also want to limit the maneuver Moment of Perfect Mind, either giving it a penalty or a drawback.
And, probably ban Thri-Kreen from the game when you use Bo9S (or just rule that Thri-Kreen can't use martial maneuvers and stances, and can't gain levels in martial adept classes). They just have too many racial advantages for using some of the nastier stuff, that would otherwise be fine for other PCs to use.
5) Watch out for a few of the feats in Bo9S, a few of them may be overpowered (or it may just be when using the aforementioned broken maneuvers that they become overpowered, I dunno). Also, probably ban the set of magic items that boost particular disciplines (like the Crown of the White Raven, or whatever it was called).
6) Disallow items that directly grant more than a +5 on skill checks, probably. Or just ban items that grant an improvement to Concentration skill checks. As long as you ban or houserule Swooping Dragon Strike, then Jump bonuses shouldn't be too powerful, so it may be reasonable to just ban +Concentration items.
7) One thing that people tend to have a fit over is a Warblade who uses Moment of Perfect Mind, Action Before Thought, Steel Heart Surge, and some +Concentration items. They think the Warblade is immune to saving-throw-related effects as a result, which is only of limited truthfulness. The +Concentration items are the main problem, though the Warblade is still tough without them; but there is a weakness to this.
They can only use each of the maneuvers once between refreshing (each maneuver can only be readied once at any given time; the slots aren't quite like spell slots, so you can't ready more than one copy of a maneuver), and Warblades have a rather small allotment of 'maneuvers readied' slots. So a Warblade who readies this, around 5th-level or so (which is around the first time that they can have all three), will also have hardly anything else readied, so he'll almost always be like a Fighter with fewer feats, later access to Weapon Specialization and its ilk, and just a tiny bit more HP.
Just because he'll want to keep these defensive maneuvers ready on the off-chance he needs them, which will usually mean consciously choosing to sacrifice most of his cool and useful fighting ability for the sake of a little bit of 'oh @&*#^$ save me!' capacity (that may or may not succeed, but usually will).
They'll be able to probably save themselves from one Will save or Reflex save effect, or one other nasty status effect, but then they'll be nothing but said Fighter with fewer feats afterward, until they refresh maneuvers. To refresh their maneuvers they'll have to be in melee, and avoid using any maneuvers that round, so they'll be vulnerable to saving-throw effects and status effects that round. They also can't change their Stance on the round they refresh maneuvers (nor on any of the rounds in which they use one of those save-my-butt maneuvers, since they all use the character's only Swift or Immediate action for the round).
So, any time the Warblade shakes off a nasty magical effect that the opponent believes should have taken him out of the battle or hurt him a lot more than it did, the opponent should be aware that NOW is the time to really let loose with the big save-or-die or save-or-become-useless guns. Never throw a single Will save effect against a Warblade; if you're going to bother, throw 2 of them in the same round, or 1 each round for 2 to 3 rounds in a row. That will overcome his ability to save his bacon once per 2 rounds (at best; sometimes he may wait even longer before refreshing maneuvers).
