First thing I would change is wound allocation, omg the current way is mind boggling slow and easy to abuse. I would mix it with 5th and 6/7th ways to allocate wounds.
Allocate one wound at a time from closes model to furthest model, repeat until all wounds are allocate. You can only allocate wounds and remove models from the maximum distance of each weapon fired (you would fire all the weapons at the same time, the current 7th edition firing is super easy to abuse and lazy rule design). Once you allocate out all the wounds you roll all characters in the unit first one at a time and choice to LOS! the rolls or take their armour saves. For all the other models roll all the wounds with the same armour save starting with the lowest armour group first (2+ saves, 3+ saves, then 4+ saves, ect) removing models with failed saves ect.

This alone would greatly reduce the current abuse of the wound allocation system and reduce the effectiveness of deathstars. Yes characters still get their LOS! rolls but you're not having one model tank a bjillion saves by itself.

I would change snap fire shots to -3 Ballistic Skill (can never go below BS1) and flame template weapons only hit D3 models.
Heavy Vehicles fire all weapons at normal even if they fire an Ordnance Weapon.
Extra Armour gives you +1 to hull points (will have Errant out a lot of units that have Extra Armour build it (reduce their cost by 15 points to compensate and increase the costof extra units that can buy it cheaper tan 15 pts to 15 pts).
I would change Gets Hot! Rolls of 1 that you can fire that weapon that turn or the next.
I clarify that Preferred Enemy affects the roll of 1 to Gets Hot! for template weapons.
Vehicles ignore the Gets Hot! for Plasma weapons (what the hell is GW thinking that vehicles Get Hot!)
I would universally reduce all Plasma Pistols to 5pts.
I would universally reduce Power Weapons to 10 pts
I would universally reduce power first/chain first to 15pts

Next I would normalize cover saves from shooting similar to Going to Ground.
I would bring jinking, firing smoke launchers, and going to ground into line as follows;
When declare Jinking, Firing Smoke Launchers, or Going to Ground; before any penetration or wound dice are rolls the unit that is being hit most declare whether they are Jinking, Fire Smoke Launchers, or Going to Ground. If so then that unit receives a +2 to their cover save (so in the open its a 5+ cover save). Any unit that has Gone to Ground can not move or assault the next turn and can only snap fire. Any unit that has jinked can move normal but can not assault and fires snap shots only the next turn. Any unit that has Fired their Smoke Launchers can only fire snap shots next turn but moves and assaults normally.
An Immobilized Vehicle can not jink but can still fire it's smoke launchers if they have not already done so.

Bikes, Wings and Jumppacks are treated as part of the model and can be shot at.
Line of Sight is draw from the models eyes.

I would fix Monstrous Creatures as follows.
MC's can only receive cover from Line of Sight Blocking terrain and have to be at east 25% obscured, this includes intervening units. In units with mixed infantry and Monstrous Creatures to determine if they receive a cover save by ignoring models in the same unit after all wounds are allocated out (if this last sentence matters)
Flying Monstrous Creatures that start on the board can not enter Swooping Mode the 1st Game turn.
FMC only Benefit from Line of Sight Blocking Terrain while in Zooming mode.
FMC's can not jink while in Gliding Mode. FMC that Jink while in Zooming mode receive a +1 to their grounding check at the end of the shooting phase. FMC's that are grounded can not assault the next turn and can not enter Swooping Mode the following turn it can move. Otherwise the FMC can move as normal.

Jump Infantry and FMCs can assault Flyers that are in Zooming mode but can only hit the zooming flyer on a 5+ in assault.
Flyers that can hover can start on the board first turn but can not enter zooming mode the first game turn.

I would change assault to 6"+D6
Hull mounted, Sponsoon, and Pintel Mounted Weapons on vehicles can fire Overwatch in Assault (most still be able to draw LOS as normal before the assault).

You can allocate up to half your attacks per pistol equal to number of shots the pistol could fire normally in the assault phase (so only one shot from a plasma pistol in close combat for example).
You can not allocate wounds in Assault further than 3 inches from the your closest model.
You can choice to snap fire your weapon in close combat instead of fight normal (does not apply to pistols) if you can fight in close combat as normal.
Chainswords are User Str, AP6, rending.
Power Axes at +2 Str, -1 Int, AP2, Concussive
The Specialist Weapon USR would only apply to models with matching sets of weapons (dual power fist or dual power claws).

I would change that Eldar and Gk's cast normal on Sanctic Powers but can't cast on the Daemon powers. (stupid GW and letting Eldar summon daemons!)
Chaos Marines and Daemons can cast on the Daemon Powers but not the Sanctic powers.
When rolling to deny blessings you roll normal as if they were targeting you and you just need to subtract the deny dice from the dice that allow the power to go off. If the total is less than the charges needed the power fails.

I think could think of a dozen other things but here are some ideas.