Combined trees were more or less an attempt to make the power investment look simpler at first glance for those who weren't interested in dealing with "rpg elements," as opposed to something like the ME1 talent screen which has a reputation of a million talents per character. Although it seems like nearly everyone agrees that in many cases the balancing wasn't right.
Since it was brought up, power combos need to be scaled back if anything. Need to either be more difficult to create (and therefore less frequent), or the damage needs to drop. Otherwise there isn't much of an incentive to make interesting powers that stand on their own merits and are useful in and of themselves. And of course the series was a little more interesting when you could Lift/Pull something and throw it further than you could otherwise.
ME1 is not the way I'd go again. That system was too basic, there were no power interactions and ... I just don't like it. You should get a substantial return for every invested point, not just a 2% increase in weapon damage. The weapon skill trees and the connected gameplay were no fun either.
The powers in ME3 and the way they work is close to optimal (except for stuff like Snap Freeze going through walls), we just need to fix tech and biotic explosions. Although I understand that without them being so strong, powers would lose all relevance compared to the damage of weapons. Which is why the powers need to get stronger and the explosions need to be dialed down. You can have either full power damage or massive explosions, but not both. I'd also argue for all primers being detonated at once, so a Throw would blow up a Tech and Biotic Explosion at the same time. With some fire on top, if you used incendiary ammo. 
Example:
N7 Fury. Current skill trees: AF, Throw, DC, N7 Fury and Fitness. I'd keep AF, Throw and DC more or less like they are now and split the other two trees into Power Dmg, Weapon Dmg, Durability and Melee Dmg.
Obviously, those trees would be rather bare without something else added to them. So Power Dmg gets evolutions that increase the damage and radius of biotic explosions, Weapon Dmg could get stability on top of more specialized weapon dmg/headshot/weight, Durability could include damage reduction, a third gate, movement speed or stagger immunity and Melee Dmg could have faster attacks, maybe combos (think of Warlord golf swing combo), special attacks or simply more boni for melee kills (we already have Power Synergy with 30% more power damage after a heavy melee kill).
Seven trees, but you'd only have enough points to max five.
P.S. The powers in ME1 and ME2 were more varied... and stronger. You could lift a Geth Prime... but aside from being awesome, that didn't actually kill it. That was left to your weapons. We also shouldn't forget that cooldowns in those games were much longer, so the powers had to be stronger for balance. Your squadmates in ME2 have 12sec cooldowns, with Liara having 9sec if you go the Asari Controller route (LotSB). She's also the only one who (barely) can self detonate combos.
ME1 cooldowns were so long, you were able to use each of your powers once during a fight. They only sped up towards the end, when you were using lvl X gear and had 50+ levels of your own. Most of the time you were simply shooting enemies, with a little crowd control thrown in. You almost never actually killed anything with powers directly.
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