Quick First Impressions
Hey! I'm super excited to have the opportunity to help you test out Atlas!
About me: I play competitive multiplayer games. I'm a Quake player at heart (top-tier player). I currently play CS:GO (ESEA-IM). I've put mad hours into RTS and MOBA games, though, like Heroes of Newerth in its prime (~1800 rating), StarCraft 2 (platinum), Dota 2, Age of Empires 2 & 3, et al.
Bullet time!
I know you guys are well aware of the pathing issues but I want to say that I do like the general feel of it and the size of the collision boxes as it lets you micro your units to get the most effectiveness out of them, and you can't just A-move your army across the map. The problem with the pathing just seems to be when a unit needs to go around another unit or a building, it just gets stuck running into it.
Gems are cool but I worry about how pub teams will do at sharing them. I can imagine the good player on the team hogging them all so the newer players can't get enough to build stuff, and also the good player raging at her teammates if they dare to take a gem she was going for. Gem spawnpoint locations will be critical to how fun collecting gems will be, I guess.
I'd like to see more variation between the squads. They're all a little bit different and have their own way of synergizing, but it would be cooler if they were each totally different and unique.
More hotkey options would be nice. A hotkey for setting your rally point, for example. Maybe one for selecting all of each type of unit to go along with the already existing select-hero hotkey. It would be nice if there was a slick way to call neutral weapons besides having a big chunk of your keyboard designated to it, especially if more are coming.
The whole multiple armories with the same upgrades system confused the hell out of me the first time I saw it. An in-game tutorial would surely help dummies like me figure that out more quickly, but it could definitely be made easier to understand somehow. For example, it would help if upgrades you already got are grayed out or removed as an option. Maybe it could all be moved to one building with one window. Something like that. It just feels strange the way it is now.
Is there a reason you have to manually spawn every unit?
That's pretty much all I can think of right now. Of course, I'll have a much better understanding of the game once I get to play against actual people and can see what the metagame is going to be like.
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To wrap it up, I want to say that I've been pleasantly surprised by Atlas. It's nothing like what I expected! I'm not sure what to think of the gold/gem system yet, but the gameplay itself feels really snappy and natural so far. I very much enjoy controlling my little "RTS squad" and doing "RTS-army-type-stuff" without needing years of experience with RTS games and their mechanics. I love that it's enough units to be an army but not so many units that I don't have fine control over it. It's a game that makes me want to "just play a few games real quick." You're on the right track! 
Comments
Re: hotkeys, there are already options to configure "select all t1, t2, t3" but they are unbound. Look in the options dialog and assign some keys to those and you're off to the races! Also, you can press 'p' to select your armory, then right-click on the map to set your waypoint, so it's kinda hotkeyed already too!
Whoa, I totally missed those hotkeys somehow! Got 'em all set up now, and it's great. Thanks!
Yeaaaah that's a bit of a worry. The cooldown helps a good bit, but we'll see how things shake out. Gem placement is something we have a massive control over, so we'll continue to tune over time.
In CSGO, many of the guns are extremely similar at first glance. But, because of how sensitive the gameplay systems are, even the AK and M4A4 feel incredibly different. This is similar to the approach we're taking -- We want to make the other game pieces bring out the different personalities of the squads. I'm hoping that the difference between squads really comes out in the PvP! Lemme know if I'm wrong :D.
Oh hell yeah it needs a better introduction for sure LOL. It's a slightly wonky representation and implementation, but I think the gist of the system is promising.
Paradoxically, making units automatically spawn caused TONS of gameplay problems. People were losing track of their units constantly. They never knew how much army they had alive. Once we implemented V things got much much much better. So, though it's a little unintuitive, I prefer it for gameplay!