Virgin lore and epic background to the mass effect universe. (including first contact war)
Yes, but we got to learn alot about the darker things in the ME universe with ME2. The first had the joy of discovery with a new IP that we knew would be a trilogy, and ME1 definetly had a more 'epic' story arc, but ME2 served its purpose, which was: learn about the different factions (Cerberus, Omega, the Krogans, etc), uncover secrets about the Reapers and Collectors, meet the main villains of the series (Illusive Man and Harbinger), and flesh out the main characters with their loyalty missions.
Complete ability to gear you and your squad mates to min/max with armor/weapon mods and armor / weapons
ME3 has a much more elegant way of incorporating loot into the game as well as customization, with a much better mod and upgrade system, as well as a more elaborate armor system. I don't think the fact that you could play dress-up with your crew and find 50 random pieces of gear in conspicuous boxes layed out around the levels made ME1 a much richer RPG experience.
More of a sand-box experience - Roaming around on charted worlds with the mako connected you with you galaxy in a more tangible way. (yes, somewhat annoying at times)
Well, I will always remember and favor this part of ME1, for sure. I agree with you, and I wanted them to fix and improve it, and I was hopeful after seeing how well they had done the planet exploration in Overlord that we would see more of that in ME3. But let's not pretend that the exploration in ME1 was anything more than a shallow attempt, and that the content on these planets was anything more than light.
Dynamic Combat Freedom - IE: Attack that that pack of geth colossus's on foot instead of with mako (or foot attack that thresher maw)
This one makes no sense to me. What is the point of attacking these on foot? I can't make sense of ME1 having "Dynamic Combat Freedom".. it was about as linear and restrictive as ME2, with the only real difference being the actual speed of combat and the difference in cooldowns, and the more obvious chest-high walls in ME2. ME1 was maybe a little more cerebral, but not by much, and I certainly wouldn't say it had freedom.