To be clear, the pain is mostly going to be felt in the first season or two of 3.0. After that, it will likely be rare for teams to be able to recruit more than 2 EE candidates in a single season anyway, so in the long run, most teams won't run into this problem. And planning for one or two isn't much of a problem in beta, unless you don't have any scholarships to work with (in that case, you really are sh!t out of luck).
For some, this is a deal-breaker. For me, I think it's a fun and realistic challenge. Early entries are all reward in 2.0, there's not much risk of having to scramble, and that risk makes the game better, IMO. I do think it would make sense to have the first cycle of the late period be signing free so programs with EEs can "catch-up", especially for players with a late signing preference. I don't think that idea is off the table.