Companion customization:
ME:A really shrank down on companion customization compared to the previous games. While I can understand dedication to specific weapons / armour due to character story and background I really didn’t like the fact that I couldn’t make improvements to my team members gear. The ability choices were frankly very lacking.
My suggestion would be to take a route similar to Dragon Age: Inquisition where each companion still has a very unique armour style while allowing for customization. I’d also like to see some freedom for weapon selection and augmentation / improvements to make companions to be even more unique. Companions should also get a wider range of skills to allow for more unique builds.
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This is one of my top 2 wishes for the continuation of the MEA series. Following the DAI template for companions as you state would allow the players to mold their companions in the direction they wanted. Changing weapons/armor/outfits and having a variety of skills, both passive & active to choose from. Both games were made in the Frostbite engine, so it's possible, but I wonder about the affects to combat balancing as the combat in MEA was such a departure from the previous games in both the ME and DA Universes. But I would love to see something done in MEA2. I hated having 18 unused skill points left over for companions (as there were no skills remaining to choose) at the end of the game. I liked the system from ME1 where each companion had a locker where you could change their load out.