In no particular order:
Must spend the bulk of their influence on Code Gate & Barrier breakers
No in-faction card draw or recursion of any kind
Shitty card support over the past few cycles - a handful of good cards, and the rest are situational to useless crap
As noted, Honor and Profit is very weak compared to the other two expansions
Every other faction spammed out Criminals' primary weapon, Account Siphon, so damn hard that everyone can deal with it much easier now due to increased Corp Econ and dedicated hate cards
By comparison, Anarchs are now stupidly powerful -they have very powerful in-faction tutoring, recursion, economy, multi-access, destruction, and breakers
Perhaps it wasn't ever that Criminals were too good, but that Corps were too weak initially...