I think playing many other RTS games and finding out what they did right (or wrong) is important.
I love the idea that you could create your own units (ala something like how Starmade, Galactic Civilizations, etc works) - but that's really going to put a tight wire on trying to balance that. Also, you would likely want to consider adding an editor outside of the regular game (from the main menu or separate program) for that feature as trying to design units on the fly in a real-time game is going to be a pain). That depends on what type of customization you're going for though, but either way - having a way to edit units outside of the game and set them up would be great.
I think Command & Conquer has always done well with its balance of Rock-Paper-Scissors. The units are clear about their strengths and weaknesses, and it makes it fun trying to break your opponents defense with your units.
I also love base building. Supreme Commander (the 1st one) is my go to game for that, and I absolutely love the plethora of units presented for use and the massive map sizes and believable super weapons (a nuke is devastating in that game). While it allows great methods for defense of your base (shields, anti-missile defense), some downfalls are that the units are all pretty generic. There doesn't feel to be a real rock-paper-scissors strategy, just mass a swarm of units and run them at the enemy.
World in Conflict is one of my favorite games - I love the line of sight concept, used really well in that game for all actions (like a sniper in a building or a forest, needs that LOS to shoot his target). The ground craters, troops and vehicles can hide in those and avoid LOS. This game was different from the typical RTS that you don't just want to rush your units in and get them killed; you want to protect them, repair them, heal them, level them and use them effectively. Especially since you couldn't just continually crank out more units; you were limited by your resource income. If you lost all of your units in play, you were at a big disadvantage to your team or, in singleplayer, it was pretty much game over. The ability to call in off map support was excellent, and the nuke, fuel air bomb, and carpet bombing were excellent.
Wargame has emulated the feel of World in Conflict, but the LOS doesn't feel the same and the game seems to go more into tons of weapons firing effects/explosions/graphics more than some of the bits of gameplay. World in Conflict just had a more realistic warfare feel to it, while Wargame tends to LOOK more like a war taking place.
StarCraft, while I don't love it the most, you can't deny the gameplay has been refined to an art. SC2 is a great example of perfecting the rock-paper-scissors gameplay, but I feel it is too similar to old RTS games and doesn't really push the envelope with anything new (World in Conflict LOS, Supreme Commander zooming the map out to see THE ENTIRE MAP and symbology).
Speaking of space type games: Sins of a Solar Empire. This game took aspects of Supreme Commander and put it in space. The original was lacking in a few ways (proper defenses) which the expansions corrected. The firefights are amazing, and the unit AI is great enough that you can just take your fleet, throw it at the enemy fleet, and watch the insanity happen as you manage your capital ships (leaders) and debate whether they should fall back. Truly, no other game has made it where you can have battles and pull your force back and attempt a retreat with covering fire while you try to save your important ships. Also, the leveling system was included which was really a boost to your advanced units. SSE also has a wonderful tech tree to it and a pretty good resource implementation, with the trading system in there as well. The pirates are an annoyance, and I wish they had included more planet types and exploration (as is improved on by Uzi's planet mod - 16 or so more planet types and MANY random planet effects). I also love that SSE lets you have a battlespace as big an insane as you want it to be. Want an insane game with 500 stars? Have at it. The ability to save-load multiplayer games has really changed our ability to have drawn out games with friends.
Graphics don't always make the game. Take Atom Zombie Smasher. Not a true RTS in the way of thinking, but it is a type of RTS that does what it does with just blocks representing enemies and your troops. A wonderful game that you can get lost in for many hours; also offers mod support so you can play it differently.
That's my 2 cents. Captcha: Without a doubt.