Perhaps no stock area-of-effect weapons, but just the ability to mod them in - and the AOE pattern, too. A pulse repeater sweep would not cause damage in a square pattern, more like a staggered line. And AOE could be used on weapons with low to-hit chances to compensate for the low TH chance. Perhaps, in the center of a square (circle) AOE weapons burst, damage was 100%. Second row of squares (hexes) out, 50%. Then 25%. Then 5%. Then no damage. Or direct hit: 100% damage, second row 25% damage.
Or perhaps weapons with cone-shaped damage arcs - think Expanding Wave Cannons which fire a concentrated wave of energy which expands cone-like, with damage diminishing as the wave travels. Or a torpedo spread, with multiple torpedoes moving in straight lines, but which together have an approximate cone-shaped arc. (Tried to make a jpeg example image, but it wouldn't paste here.)
Also think that battles should be SFC-like, with an Empire Earth perspective and zoom capability.
Also, I stick to my idea: Boarding Marines that you can design like troops. Just like the idea of designing facilities for yourself, which I also still stand by, you could design boarding components; for example:
-Small Marine Detachment, 10kT
-Medium Marine Detachment, 15kT
-Large Marine Detachment, 20kT
-Marine Force, 25kT
-Marine Army, 30kT
and you can design them with:
-Body Armor, 1kT, 3kT resistance.
-Powered Armor Suits, 3kT, 15kT resistance.
-Personal Shield Generators, 10kT, 25 shielding.
-Pistols, 1kT, damage: 1 1
-Rifles, 1kT, damage: 2 2 2
-Assault Rifles, 1kT, damage: 3 3 3
-Pulse Rifles, 2kT, damage: 4 4 4 4
-Pulse Machineguns, 3kT, damage: 5 5 5
-Grenades, 2kT, damage: 0 7 7 (they won't throw right in front of them)
-Demo Packs I-IV, 4kT, can destroy 10-20-30-40kT of comps.
-Bomb Belts, 10kT, will kill the marine (i.e. destroy the marine component) when used, damage: 15, can destroy 20kT comps.
-RPG, 6kT, damage: 0 0 10 10 10
-Shotgun, 3kT, damage: 10 7 3
-Pulse Shotgun, damage: 15 9 6 2
et cetera. Boarding combat similar to ground combat. Boarding can take several (game) turns. Boarding Troops can be reinforced and pulled out like troops. Boarding Combat can damage internal components OR crew/defenders, some weapons can attack only comps (Demo Packs and such), some both (Bomb Belts). You can mount auto-defense turrets in your ships next to security personnel, infantry troops can help in boarding combat, you can create weapons lockers to arm your crew. You can train your crew/boarders in several disciplines (Martial Arts, especially handy for crew or marines with just demo packs, unarmed hand-to-hand, Marksmanship, increases damage of weapons as they aim better, Sniping Skills, extends ranged weapon range as they will now take the chance of firing while the enemy is farther away, which they otherwise wouldn't for risk of damaging vital components or blowing a hole in the hull, atc.) to make them more effective in combat. Space Marines should also be able to fight ground combats.
Sorry if the above is unreadable. I'll try to put it in a handy .txt file if you ask