Play 1v1 games. They have the greatest educational potential. Try to play 2vX only when you're on voicechat or in the same room as your partner.
Disable the sky and the backgrounds, even if they look very nice. You want to clearly see the small pieces of terrain debris that will occur in one way or another.
Play small tactical maps. Lurk is one of the best of those that come with the game. Other good choices are Below and Chill, and also Octogame, in case you can cope with the black holes (you will think they consume your clones even if they're 1/2 of the screen away). Select same gravity for both players. If you play on such smaller maps, zoom out until you don't have to scroll for the entire game.
Choose the highest route that is still safe. In Lurk, this is the route that goes directly below the cage trap that swaps control of the clone. Any lower route can be easily attacked by saboteurs that are dropped one at a time from the higher route. Any route that goes above the trap can be attacked by loppers from the aforementioned route, which is worse for the upper route here than for the lower one because of the trap.
Multitask. Know what is happening at each location, and multitask. Multitask as much as you can, because...
Awareness/attention is a resource, similar to alive clones and skills. Harass to force the opponent to react, which might hinder him elsewhere just because of the spent attention. Harassment is good wherever a lot of enemy clones are. The best point is usually the enemy hatch/entrance, since he can't route around that point. Adapt an annoying playstyle. This is very much like harassment in a real-time strategy game.
Terrain removers are much stronger than terrain adders, this is why sabotage works so well. Alternate between driller and basher assignments to the same saboteur to trap clones and prevent opponent builders. Builders will fall when they aren't standing on anything.
Do not explode saboteurs if you can't replace them easily. If there are no saboteurs in a given zone, the opponent doesn't have to spend as much attention there as he would even if you'd just hung around with an idle saboteur. If you lose saboteurs, you narrow the opponent's cone of uncertainity in the given area, which you want to keep as large as possible. Explode saboteurs only if you will gain a large benefit that compensates the opponent's gain in attention/certainity. The best example is again hatch digging: The digger's tunnel is very thin and easily countered with atomizers, the exploder's terrain removal is large enough to cost several atomizers and/or micromanagement, thus attention.
In general, don't use exploders/atomizers unless the benefit is greater than the loss of the specific clone. You should conserve as many clones as you can. Try to put blockers on removable terrain so you can go and free them later if necessary. If you don't want this grind factor, play only highly tactical maps, such as Lurk, where a good number of clones will die for sure...
If your clones get bunched up, Lemmings-assign a basher/gulper/whatever in combination with directional select. Lemmings assignment consists of holding the skill key and the directional key at the same time, and click on the bunch. The related term of spam-assigning means to spam Lemmings-assignments to the bunch, e.g. when you want to assign a lot of floaters or spinners. You might want to use a hotkey layout similar to mine for this, see the other thread in this forum area I made. (I personally think that the regular assignment in Clones combined with the optional Lemmings assignment isn't as useful/comfortable as having just Lemmings assignment without having to hold down two keys all the time. To a bunch, you always want to spam-assign to save time, even for precision moves; to separated clones it doesn't matter unless you are queuing skills. I'd even give up the ability to queue skills for this.) Basically, learn to Lemmings-assign at least in the proper situations, it appears to be the best way of assigning skills.
More will follow when I can think of more and feel like writing again.