It's not just what the game's doing, it's how it's doing it. The UI, the feel of the movement, the structure of missions and exploration. It's like playing a late-gen 360 game (at best). It feels like the developers haven't tried to grow and evolve since Saint's Row 4.
If this game had been released a year or two after SR3 or 4 it wouldn't feel out of place at all. But now, it feels dated. There's been a lot of iteration and growth on all of the things this game is doing in the multiple genres this game is trying to take a stab at. This game doesn't reflect any of that.
I'm not saying the game is bad, but the RPG mechanics you're talking about are also part of what makes it feel dated. There's a ton of fiddly customization stuff that you access through this really nasty, complex UI. They should know how to present that stuff better by now. But they're still showing it to us in the same weird, unnecessarily complicated way that the last two Saint's Row games did. Everything's buried in menus upon menus and you can't get a good idea of what's happening to your character overall without sorting through a bunch of different sub-categories of buffs and systems. Hell, Borderlands 2 had a better UI for this kind of thing and it's UI sucked too. And that was years ago.
And that's on top of the shooter gameplay feeling like Crackdown 1. Which is a fine game. But an aged game. Attacking enemies isn't particularly satisfying looking (except as melee characters, which are pretty genuinely enjoyable), and most of the game's missions are "go to place, shoot guys. go to another place, shoot more guys" instead of having more story or structure to what you're doing. You're just killing random minions while the story happens by way of NPCs telling you things via voiceover. You effectively don't matter, the game's an audiobook with boss fights and busywork.
The sandbox/shooter genres deserve better than Agents of Mayhem.