Forum Discussion
While I suspect that the Benefactor arranged for most of the evidence of the Initiative in the Milky Way to be eliminated, most of the major covert intelligence organizations were tapped into the Initiative, a fact that I believe is at least partially confirmed by some of the characters we meet. If you read the Benefactor speculation threads you will see quite a few possibilities for this group, besides the obvious government agencies. Even assuming that many of these groups lost their Initiative records or didn't have the resources to pursue this option on any scale, that would still leave several who could covertly create at least small arks without being noticed, similarly to Cerberus creating Normandy 2. As for other arks, after the assault on Earth, I suspect that Liara would use her resources to begin creating them, either as lifeboats or as a way to leave the sorrows of the Milky Way behind. In the latter case, one of the arks may wind up containing Liara and her little blue Shepard.
Some more ideas.
Melee dash powers:
Biotic Dash- discharges a biotic wave that has chance to knock back enemies in a small area
Tech Dash- discharges an electric pulse that has chance to stun enemies in a small area
Combat Dash- additional melee damage, ignores shields and armor
Sidearm:
Like a melee weapon, this is a free weapon slot for all characters but it must be from the pistol category. For the Pistols upgrades at level 6 one of the options becomes Dual Wield, where the character can use two pistols at once (no additional bonuses for the level). The pistols must be the same but the player does not have to craft/purchase a second one.
Ensnare (combat power):
Temporally wraps a small enemy in reinforced wires preventing them from attacking and increases damage against them
Bolts (tech power):
Unleashes multiple small electric bolts that damage enemies, lower shields and have a chance to stun
Echo (biotic power):
Creates a biotic apparition that appears near enemies, distracting them from the player and attack the apparition
Heat Sink
When customizing a gun, give the player a choice of using the vintage heat sink that recharges or the modern one that discards rather than the vintage being an augmentation. Reduce the magazine capacity penalty of the vintage but increase recharge time
Base Armor Layer
Have the basic, underlying armor be upgradeable also; think like the Medical Exoskeleton from the original ME. This can have different upgrades than the outer armor layers.