A lot of the ideas here are quite good, and some have come up before in various places, but I suspect that some of them could be used for cheating by some airlines.
Donations and alliance bases could be used to overcome current limits on base numbers - for example, I could create an alliance for just myself and funnel all the fees into opening up more bases than I am allowed, as alliance bases. This could potentially be overcome by tying the number of alliance bases to the number of airlines in the alliance (say one extra alliance base per airline in the alliance).
Resale of airlines is a dodgy one. It has been suggested before that inactive airlines be offered to sale to the other airlines. This has been turned down on the basis that, firstly the purchaser may not be able to take on all the inactive airline's bases (as they would end up with too many bases) and secondly, they likely wouldn't want much of the airline anyway (there would be lots of old planes, on routes which need to be edited for a decent LF anyway...).
The idea of having alliance planes also has quite a bit of potential for cheating in the fact that one person could set up a series of extra airlines for themselves, then deactivate them, or make large donations from them - and effectively give all their assets to an alliance, for the benefit of their main airline. The current alliance system is limited so as to prevent the potential for multiple account cheating.
Something along the lines of an alliance market has been suggested before, and sounds like a great idea. Rather than being a separate market (though that might well work), previous suggestions have asked for a "sell to alliance members" option - selling through the regular market, but like private sales, which are only available to/seen by one person, they can only be seen by your alliance members.
In terms of trades, I tend to think it isn't worth it. People will prefer to have cash, especially in the context of AM, where 2nd hand aircraft are generally sold from large airlines (who want to buy shiny, new, big planes) to small airlines (who want to buy something bigger than they could normally afford - and take the trade off with higher maintenance). There would be few circumstances in which a small airline would have a plane a larger airline would want (as the planes the small one are retiring would be far too small for the big one). There could also be difficulties with the AM accounting system (which is based on cash transactions), though you may be able to work this out based on aircraft values or something of the sort. There would also need to be checks to ensure the aircraft are not too far apart in value (with the potential for money transfers between cheating airlines), as currently takes place based on aircraft value.
