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1) Better terrain / line of sight rules. The terrain/los rules have been getting worse since the high point of 4th.
2) Alternate Activation, or at the least something like I hear Apocalypse did with taking casualties at the end of a turn.
3)Bring back USR. 15-30 tightly worded ones should really give enough life to things. Instead of 10 different bodyguard rules, just do "Bodyguard X+" where they take a hit for a character on whatever X is in that rule. Same with the multitude of "-1 damage" abilities and the like that show up. Each codex can still have its own special rules, and even some specific units can have unique ones, but having a core of universal special rules to fall back on makes things much simpler.
4) Make all named characters specific builds of a generic character. Give characters lots of fun rule options they can purchase so you can say run the unit cheap, bling them out with gear, or buy up some special rules or buffs to them. Reduce auras (they can live on, just not be as prevalent as they are), make it so characters can say impart a USR onto one or two units. Hell, let characters actually take fun options. A guard Company Commander can take a power fist or a plasma pistol, but cannot take a meltagun that is in the same kit? Why not, its not like it would be gamebreaking.
5) Stratagems. They are getting tiring figuring out just what is what, and wargear being tied to stratagems, etc. I'd say get rid of them entirely, but even just cutting down the number severely would help.
6) Make leadership matter. Self explanatory, with each edition it has meant less and less. Give it some importance. I'm not saying go back to 4ths way of only being able to shoot closest enemy without passing a roll, but bringing suppression into the mix could help.

The problem is stratagems are tied to such a gamey mechanic at this point its hard to think of them *not* as a unit in an rts game with a cool down.

When in my minds eye I think of a stratagem I think more of an overarching plan, not "unit X can shoot harder suddenly so units Y and Z cannot do that now." It doesn't help that things that would actually make sense as strategies either already exist in the game (a forced march is basically advancing - the unit gives up certain actions to move up farther) or don't exist at all (digging into a defensive position), or are under the domain of a single faction (crossfire). If "stratagems" were reconceptualized in the context of...blanking on an actually good term so for lack of a better one demeanor, of a unit, that could at least make some sense. Say like "standard", "offensive", "defensive" and "forced march" as just examples. You declare the strategy of each unit at the start of your turn, then begin implementing your actions based on what your plan is. Could work with both I go you go and alternate activation - maybe if command points must still be a thing, they can be used to force change a demeanor mid turn in reaction to what your opponent does in an AA setting, but with the limit of command points you can only do it so often.