Re: Fleet merge order.
That would be quite useful.
Re: Multi-ship build
Technically, its only because they are units (and quite small) that you can build in batches, and ships aren't units.
For a mental image of why, think of Earth today: mines, tanks, and (commercial) sattelites are all built in bulk.
Ship construction ties up a major facility for quite a while.
I'd also imagine that the one-ship-per-turn constraint helps to avoid certain unsavory tricks.
Imagine if you will; in the late stages of a game, a player prepares for war... on his planets, he orders construction of 1000 dreadnaughts, holding the queues at 1 turn from completion.
The fateful day arrives, he unholds his queues, and unleashes 1000's of massive ships without:
1) having to pay maintenance
2) having to pay unmothball costs
3) having ANY indication of his strength appear in score or intel reports.
After a few quick 1000 vs 50 skirmishes, he wipes out his opponent's resistance, and then scraps some ships to pay maintenance.
The odds drop to 200 vs 20 or so, while he walks through his opponent's homeworlds.