For Morale:
Pinning test for each time you are shot at, with any of the applicable modifiers: -1 for taking wound(s), -1 if the weapons are pinning, -1 if you are in cover (more likely to duck if there's something to duck behind), -1 if the weapons are heavy. If you take 25% casualties, then test to fall back, even if you were previously pinned. Modifiers for this test include: -1 for each enemy unit within LOS and 18", -1 if under 50% strength and -1 if not in cover.
Then in assaults, Ld test for losing the assault. Calculate assault winner based on wounds dealt, factor in outnumbering (+1 if you outnumber, +2 if 2:1, +3 if 3:1, etc.). The losing side must take their leadership test with a negative modifier of how much they lost combat by
For Saves vs. Weapons:
Subtract 7 from the AP value of weapons to give the save modifier (AP 5 makes you take a save at -2 to your roll). Cover would add to your save. For example, 4+ cover would add 3 to your armor save, so a terminator would have a -1+ save, which could then be reduced by an AP 3 weapon to a 3+ save in total.
For Movement:
Different move and charge speeds for different races/type of infantry. ie. terminators are slower than power armor which is slower than scout eq. armor which is slower than flak armor. Also, running just flat doubles your movement, DT slows it by a certain number of inches.
For Vehicles:
Do away with the utter stupidity of CC always striking rear armor. Make them able to fire more on the move (today's tanks can move faster than these things can and still fire accurately). Also, if ramming is kept, it needs to be able to make capable of causing >S10 hits.
EDIT/ Vehicle cover saves should go, but should be replaced with an increased chance of glancing rather than penetrating. Basically you would get +1 to AV for each full 6" of movement over the first 6, and +1 for being partially obscured from the firer's LOS. This AV change would not effect whether you could be dealt a damaging hit, but would make the odds of a glance higher than those of a pen. For example, versus an AV 12 fast skimmer moving 24", a railgun would still glance on a 2+, but it would only pen on a 5+. So you would still use AV to tell whether you had been hit with a damaging shot, but actually being hull down or moving fast would confer more realistic advantages.
Also, Blast weapons should maybe be able to damage troops in an open-topped transport. /END EDIT
For Missions: Bring back the old types and do away with the nonsense of only troops (and everyone else's special cases) being scoring units.