1) We already know that Inno doesn't want ghost guilds to exist so this is yet another action that restricts their abilities (not 100% effective on it's own I know but it does somewhat impact their effectiveness).
2) Is it reasonable to expect that every player should be allowed to respond to sieges in EVERY age with any combo of troops they want? Personally it might add a bit more to the tactics and planning guilds go through if each member can only retain enough troops to cover a few ages at the same time. Another side to it is we now each have the exact same limit to the troops we can get, we know that a single player can't cover all ages alone (they'll need to work as a team). So suddenly all those guilds that own sectors in every age are much more appealing targets as they are now bound to have weak spots. No more infinite troops to be able to retaliate regardless of the age attacked.
3) Your Alcatraz would have to give you more than 2000 unattached units per day for it to technically be constricted by this unit cap. All it means (assuming you get your alcatraz to such a point) is that you no longer need to care if your troops live or not, because the very next day your alcatraz will bring your troop total back up to the full amount. Sure as it gets to the higher levels you might miss 1 or 2 (and as it gets higher more and more) collections but it just means that as soon as your pool of troops drops to below 2000 you can instantly top it up (once again adding to the whole "no fear" idea behind using troops)
Edit: the above are NOT the core reason for the cap (which is the game stops working with too many troops), they are side effects of bringing in the cap. So this post is about are these side effects actually bad? or is it that a cap for solely the above reasons is bad?
1) the notion that only ghost guilds are capable of multiera mass expansions in one day makes no sense. Many guilds make massive moves in multiple eras on the map. And since people in IA will take more damage in IA GvG than people in CE with 90%+ attack boost, it does make sense that a higher player would be in multiple ages during a multiera expansion. And until ghost guilds are prevented from existing, or people get banned for being in one, they do exist and it is a valid (though as you say, not intended) way to play. Not many people like that (myself included) but there it is.
2) reasonable? of course not but even in big guilds because this is a 24/7 game sometimes there is only one person on at any particular moment watching the map, so having the ability to respond in an era is kinda nice (and thanks to the rogues, don't need 2,000 units to respond to a siege as was already pointed out.) Personally I can fend off, or at least poke at, a siege from three quarters of all the eras so far.
3)/the rest of it. I was refuting starzaan's logic, not supporting anything or trying to discuss side effects. I don't know if the side effects are good or bad. I am not deluded enough to think it will make a difference to ghosting much especially since it is an incentive to burn through troops, but I don't know if it is a good thing. As the game currently allows us to play, there are valid reasons to having more than 2,000 units. If one were to take the original argument to the logical conclusion, saving unattached units is not a valid thing to do ever, because if you aren't using the units right when you collect them what is the point?
The point is to save them for when they are needed. That is at least why I have a traz. The reason to have more than 2,000 units is so that when you need them, you have them.