As written, yes, aptitude means any feat that works on any weapon, also works with your aptitude weapon. Not only is this preposterously powerful,1 it’s not hard to imagine cases where it gets flat-out nonsensical. But it does allow for a huge array of potential combos and tricks, particularly things you couldn’t have done otherwise, and that means the rules-as-written aptitude is of significant interest in optimization.2
In practical terms, just for the sake of both balance and sanity, aptitude should probably be restricted to only working on feats that let you choose what weapon it applies to, and for which the aptitude weapon would have been a valid choice. This is probably what the authors actually meant for it,3 seeing as it’s quite similar to the warblade’s weapon aptitude feature in the same book. Under this houserule, you can use Weapon Focus (hand crossbow) for your aptitude great crossbow since Weapon Focus (great crossbow) is a perfectly valid choice, but you cannot use Hand Crossbow Focus on any great crossbow.
This will often mean that no one will bother using aptitude, since +1 is pretty pricey for that and auto-proficiency, but that’s OK: most special weapon properties out there get ignored. Aptitude will still have its place for those who want to use some exotic weapon without the feat and want to have any feats they were using prior to being able to afford aptitude still work with the new weapon.
My other suggestion for handling aptitude well is to consider the specific use-case for which someone brings it up.4 To allow certain feats to work on an aptitude weapon even when they would not otherwise be a valid choice, on a case-by-case basis, is probably good for the game. Plenty of feats are written too narrowly anyway. But in such cases, I would consider waiving the need for aptitude in the first place, and just allow the feat to just work with that weapon to begin with.
And it gets much worse than you suggest: Hand Crossbow Focus on great crossbows makes for pretty hefty damage, but Lightning Maces and Roundhouse Kick on high-crit-range weapons results in statistically infinite damage.
In fact, in terms of a feature having little purpose besides opening up ridiculous tricks and combos, aptitude is probably second only to the Snowcasting feat from Frostburn.
Though HeyICanChan poses an interesting alternative: “the majority of Wizards of the Coast 3.5e books assume the reader is only using the core rules and that one book (itself a drastic overreaction to AD&D 2e's you-must-own-all-our-books-to-understand-this-crap policy). Viewed in such a light, aptitude is a workaround allowing a long-played PC to use some weapon-specific Tome of Battle's options without modifying the character to fit the newly purchased book.” This may very well be true, and if so would fit nicely with the feats in the book for the weapons associated with one discipline or another.
As an aside, this advice works for most broken tricks in the game. Plenty of times, players turn to broken tricks to make up for deficiencies in the rules. Don’t allow the trick, but consider strongly whether or not it would be a good idea to fix the problem they were attempting to patch with the trick. Often the answer will be yes.