I would like a major overhaul of the rules. These changes fall into the following categories:
Scale:
I would like to see the removal of titans, superheavies, flyers, knights, and anything else which was previously confined to Apocalypse or, for those old enough to remember, Epic. All of these unit types are too large for the 28-30mm scale that 40K uses, make a mockery of the range and armour system, and cannot be accurately represented in 40K without causing major issues with internal and external balance. If players want to field these units, play Apocalypse or Epic. The latter, in particular, is much better suited to them, and it's a lot more fun using these units at that scale.
Army List Building and Force Organisation:
I would like to see a return to one Force Organisation Chat and one way to build armies. All these different ways of building army lists, formations, detachments, or whatever else they are called these days are confusing, make it difficult to play spontaneous games, and do not, in my opinion, improve the quality of the game.
Reduce Dice Rolling and Randomisation:
This applies to psychic powers, rolling for traits, and anything else which involves unnecessary randomisation. I'd like to see a return of points values to pay for abilities such as these, rather than randomising them. It would speed the game up and bring back the tactical element of choosing the right power or abilities, rather than being at the mercy of the D6.
Psychic Phase and Powers:
I agree with those calling for this to be revised. Powers need a major overhaul, in particular, as some are way too powerful, while others are very ineffective.
Stop using the D6:
This is controversial, as it goes against the founding philosophy of Warhammer and Warhammer 40,000. The idea was that the game could be played by anyone who had six-sided dice lying around the house or from any boardgames that they own. The problem with the D6, however, is that it makes it very difficult to accurate respresent the differences between units. D10s or D12s would be able to achieve this more effectively. Even better, however, would be to convert to a percentile dice based system and state. That really would make it much easier to represent elite and regular units, for example.
Reduce the number of special rules and overall complexity:
The rules are too long. I would like to see their number reduced by adopting an Age of Sigmar type approach, although possibly not quite as reductionist, to 40K. My view is that 40K needed this kind of treatment far more than Fantasy did, so GW missed a trick in not implementing this approach with 40K.
Allies:
I would prefer this system to be removed completely, but if it were to be kept it at least needs to make sense. There needs to be a table governing which armies can ally with each other and it needs to make sense from a background perspective.
That's about it for now, but I'm sure that I'll think of some more ideas.