1.) The planet scanning is a good conceptual idea, but wasn't flushed out enough to make it less tedious.
What I would change: At the very least, I would allow an upgrade that let's you have a better visual cue of resource deposits. The look would be similar to a thermal image, with certain colors corresponding to lode density. Just one point of interest though for people. Element Zero is rare, but you don't have to scan a planet to find it, read the planetary biography, any planet with a prior settlement (Current or ancient) is very likely to have Element Zero. Other planets are less suble about it, like "An asteroid laden with Element Zero impacted the surface".
2.) Trivial exploration. The Exploration could have played a vital role, instead, the fuel system is incredibly trivial, and tedious. While I enjoy buzzing around the galaxy in the Normandy instead of a cursor, the actual mechanics remain the same. A broad example of how it wasn't done right can be seen in the fuel upgrade. A completely useless upgrade, since any cluster in the galaxy can be reached on normal fuel.
What I would Change: Much deeper exploration. One point of interest is that Primary relays between clusters should be fixed one to one. What this means for exploration? You'd actually need use that fuel to cross the galaxy. While I'd say link primary sites with the omnidirectional Secondary Mass Relays, deeper exploration requires taking chances, and crossing over star clusters to find another primary relay. This could also be a "Big Choice" moment. Do you activate the dormant mass relay, and risk exposing the galaxy to another war? Or maybe there is secrets beyond this relay that could help in your endeavor, or maybe both?
3.)Weapon system. While I have no issue with the actual limiting of equipping weapons and armor only on the Normandy (Or before a mission) the actual variety is fairly bad. Armor not so much, the OP points out that there is only 1 set, which is an incredibly linear way to look at it. To be fair, if you use Mass Effect 1's definition of "Armor" to Mass2, there's probably somewhere in the realm of 140,000 different armors. Maybe the argument was more for stat-****s looking for arbitrary number boosts that are moot, since you can just take cover. Though some progression beyond would be welcome. As for the main point, about weapons, weapon statistics are much more important. Basing weapons solely on "feel" is a disservice to the RPG and Shooter fans alike. Look at Modern Warfare 2, there is the basic "Feel" weapons, Assault Rifles, Submachine guns, machine pistols, ect, but among them, are several iterations with different strengths.
What I would change: Should be obvious, I hate to cite MW2 for anything, but that's a very good example. How the weapon system works would require a little finesse in execution. At shops, instead of "Buying guns" you buy the fabrication rights to that model, While an individual weapon may only cost 150 credits, the fabrication rights (which is what you are buying) so the Normandy's armor can reproduce them, cost significantly more (10,000+ or what have you). Some weapons that the developers "Intend" you to get at certain times should be available, albiet at prohibitively expensive costs (IE Tempest SMG) so a frugal player could invest to have a powerful weapon early. It bears some mentioning, that I do like the "Upgrade" system, this is much better than finding Version 1-10 of a weapon, and makes more sense from an imerssive point of view. What I'm asking, is weapon models with different stats. A base example would be assault rifles, Elkoss Combine's Avenger being the standard, balance, where Elanus Risk Control's Banshee would offer more accuracy, better cooling effeciency (More shots) but lower individual stopping power and fire rate. Kassa Fabrication's Breaker would offer unparraleled stopping power and accuracy, at expense of a very low cooling effeciency (Ammo capacity) just broad examples.
That's enough textwall for now.