Currently, there are many disadvantages of being in an alliance, but few tangible advantages...
For example, an alliance member:
1) has to pay fees
2) must coordinate with other alliance members about oversupply, since all alliance members are counted together
3) cannot sell planes to other alliance members at significantly higher than market value prices, even if planes to non-alliance members would be selling at this price (like an A320/B737 at the beginning of MT)
In order to counteract these disadvantages (which all probably have to be there in order to maintain rules), there should be some tangible advantages to alliance membership.
For example, in AWS, you can't supply over 200%. In the real world, an advantage you could have on the same route is you could have a JV with the other carrier, and/or you could codeshare so that their flight also becomes yours.
In addition, SkyConnect has been advocating for a long time (although I don't think we ever put out a formal feature request) that alliances should have a central fund, that airlines can contribute to when they are profitable, and draw from when they are in trouble. Allowing strong airlines to support weak airlines is something which we feel is very important. It's advantages like these which would make an alliance actually worthwhile, compared to the state which they are in now, where alliances are largely a burden on the airline rather than an advantage. SkyConnect could open a free forum on another website right now (phpBB is very user-friendly), and be done with the alliance concept altogether. This would mean that:
1)don't have to pay alliance fee any more
2)don't have to worry about accidentally oversupplying routes
3)no restrictions on the profitability of aircraft sales - airlines can sell to each other at the going market rate rather than an arbitrary restriction (10%). I remember in the beginning of MT5, I could sell an A32x at 130%, and it would be gone within 2 minutes. Taking a 20% cut to my profitability, especially at the beginning of the game, is a real motivator to sell outside the alliance.
I do hope that a solution can be found where alliances can be useful, but not required for successful gameplay.