I honoustly dont see a way for the MA to ever become usefull to me, unless they come with something out of the box or something thats goes agains normal game design I simply don't see a way.
Unless we come up with spells that give permanent improvements like for example the size of your city coffers, reduction of scouting costs ect.
Spells that break the barriers that are designed to keep us players in check.
Lets analise the other madatory buildings
-City Hall
A start building, everyone has it, it's also a good source of points for your ranking, and with each expansion more points can be gained. it also decides the size of your city coffers, the amount of hammers you can store and some premium gimmicks
-Builders Hut
Again a start building, one of the most useless ones but since it's a start building everyone has it. it decides how many builders you have, having no builders would ruin your game, therefore essential. the building is designed to be unable to mature but as a start building this is not a problem.
-Barracks
A building that over times matures, while those who dont like to fight feel it's useless, it's still a mayor source of ranking points, since it's a maturing building if it becomes to useless there is always the option to improve the building to easily make it worth while.
-The Trader
A building you need to build, a building who at start looks not the best building on the planet, and is designed to not mature (tho maturing options are possible) but when your game matures and your production bonus on bonus goods improved it becomes really difficult to play without it, not impossible just very very hard. therefore a building few people question.
-The Magic Academy
a building that you do not start with, it's large cumbersome and like the builders hut designed in a way that disallows maturing, a building thats questioned by many to be forced to be mandatory, Unable to mature due game design, and for many a building with spells that are worthless in mid to late game, more usefull early game.
1. Solutions: spells that break the game barriers.
2. Making goods in need so much that the only way to handle it is to use the magic academy to boost your goods production into managable levels. creating a game barrier that can only be broken by the MA --> returns to point 1.
Sidenote: designers should have taken notice when the problems around wonders where revealed, the most popular ones are Mountain Halls and Sanctuary, both buildings "add" points to the people ranking, dwarven bullwark is one of the least popular ones. this is very wel recognised by the dev team and solutions have been thought up / still under discussion/implementation. the MA has actually the same flaw yet no one in the dev team seemed to have acknowleged that fact. a 2x2 spire (fits the theme, wizard towers are very famous in fantasy stories) instead of a huge building could have eased the resistance agains this building by a lot, and is actually still an option since you can always shrink down a building (expanding it creates issues) A 2x2 or 3x3 building fits very well in city design to be combined with buildings like the builders hut fitting the late game layouts.
Edit: a portal to the "Elvenar Magic Acedemy" would be even much better, it would create a easier way to "shrink" the building, and looking how "rare" magic acedemy's are in fantasy stories. it would fit the theme as well.