Tyranny actually had a decently complex spell system with a long list of various effects, durations, way to change those durations and effects, etc. It only seems really simple if you only acquired the simpler spell sigils. Hell, you can build your spells so that even your basic fire spells inflict three status effects and have wildly variable AoE's from standard.
Classless progression systems are also inherently more complex than class-based. Tyranny did simplify some areas, but I don't think its problems can be primarily attributed to simplification.
Anyhow, complexity is, all else equal, bad. Adding complexity to a game is justifiable if it adds interesting gameplay, but lots of complex features provide little or even negative value to games. I don't think Pillars had any obviously negative-value systems (it seems like the stronghold was this for some people, I guess), but I do hope that Obsidian has looked for areas that didn't produce returns commensurate to the added complexity for reworking or elimination in the sequel.