The problem with just increasing the number of bookmarks is that it both increases the amount of work to deal with them (1000 or 2500 items is a non-trivial amount) and it increases the back-end load on the servers.
Remember the main thing that got rid of Warp to 15 wasn’t that it was frustrating and arbitrary, it was that the bookmark load on the servers was killing performance.
Creating bookmarks that disappear on an interval when the thing they’re marking is no longer there would work fine.
Alliance bookmarks are another thing entirely and, IIRC, have to do with how Alliances work as entities in client code. Otherwise they’d have made it into @CCP_karkur’s list of little things.