Generally homebrewing modifications or adding/removing a rule here and there for expedience will be fine if you're just playing with your close friends, as chances are they'll have encountered the issue with you and agree it needs fixing. Wargaming is socially a little different from MtG (at least outside the USA, Americans generally seem to be a lot more competitive about TTGs) in that any non-tournament game is probably "casual".
Homebrew stuff is usually right out for "pick-up" games with strangers of course (but I doubt there'll be too many of those until AvP hits retail), the issue usually comes in if you have a fairly large gaming group, and it's generally mid-term players who have a problem with it - veterans know the faults in their game systems and will have probably been homebrewing themselves, and the n00bs love the creativity of adding to the game mechanics (although will almost always go overboard if they attempt it themselves
That's all anecdotal though. I've just had a lot of problems in my time with people assuming that any
modifications you've made to a unit or rule is solely to benefit your chances of beating them, as opposed to balancing the game for everyone, or adding a really cool idea, in as fair a way as possible.
It doesn't seem like there'll be a huge need for it with AvP factions though, as the figures will come with their own stat cards, and leaders will change the way the force works. The way I've interpreted the Predator clans so far is that if you take a Berserker, its' rules change your other Preds into BSPs or Hish or whatever they're called, as opposed to standard Predators. It's a simple solution, and while I don't follow the Predator mythos the same way I follow the Alien one, I can't see anything wrong with the mechanic.