I personally think Autumn Dynasty and Anomaly 2 are the best ones right now. Although some may argue Anomaly 2 is a defense game, only reversed. I think there is enough offensive interaction in A2 to call it an RTS, but that's just me.
I've really been liking Oil Rush a lot lately too. A little simple coz of the auto-battles and auto-training of units, but looks really good, and definitely plays as an RTS. It includes the usual stuff... Expansion, exploration, fog of wars, unit upgrades, etc.
Exact-Psience My 2014 Top 10 Games of the Year: Monster Hunter Freedom Unite, Hearthstone, VVVVVV, Battleheart Legacy, Wayward Souls, Bug Heroes 2, Powerpuff Girls Defenders of Townsville, Deep Loot, Monument Valley, Bioshock Honorable Mentions: Traps N Gemstones, Bardbarian, Goblin Sword
robocalypse is not bad, a bit short but has all the elements you are looking for. Rise of lost empires was enjoyable but instead of collecting resources, your buildings generate money and you build farms to increase the number of solders you can train. First you play as humans and then you can play the orc campaign. I just started Art of War 2 Global confederation and its not too bad so far.