I don't think the waiting time is inherently a bad idea. If anything, it could be a net positive for immersion and the whole "consequences" thing. However, that depends on two things:
1) Accepting that you are actively denying your players to focus on a single thing (ex: planetside 2 with the nanites required to get a tank/aircraft, and if you lose it quickly, well, you may not have enough for another immediately, so off to infantry you go). You really want to think that one over because it's fairly negative.
2) Having enough alternative gameplay loops taking over during that waiting time, and well, they're pretty short here right now.
I sort of agree with the person who posted that it made no sense to implement now and should only be added later, but am not sure it's quite as simple. The alpha/pre-alpha/whatever-you-call-it is the game, and will be the game for the long foreseeable future. The longer it lasts, the more comfortable the playerbase grows, and the more hostile it will be whenever you try to introduce such a change down the line. So in a way, taking the pain/unrest now is not a bad decision, provided that they thought it through. To go back to planetside, the limit ensures battles can not degenerate into all tanks all the time, and ensures a constant high supply of infantry players which is critical to what the game aims for. I'm not quite sure what the point is here to tell the player that he'll wait 3h for his Carrack. The player clearly doesn't benefit from it, so it has to be the greater game benefiting from it, but how?