My real favourite turn based systems are tabletop ones.
The ones that I feel particularly work well are Confrontation and Alkemy, two fantasy skirmish games, each with their own little twiddles on the concept of turn based combat.
Both are alternating turn games. Each player activates and uses one unit then passes over to the other player, rather than one player getting all their activations then the next player getting all of theirs. The latter system tends to be heavily biased towards whoever goes first, especially if they have some particularly strong attack available. Infinity, another tabletop game suffers from this, with grenade spam allowing you to wipe out half an army in the first turn by simply activating your TAG over and over and using the speculative fire rules (firing over cover). In videogamespace, Valkyria Chronicles is weighted down by this. Scout rushing is the most viable and powerful strategy late game, and generally it's an odd map if you're not just pumping all your activations into Alicia and leaving the computer with little to no way to respond. It also has the problem that when it's not your turn you are essentially a passive observer, unless the game has a significant reactive component (Infinity has reaction fire, but it overdoes it, bogging the game down). So, an alternating turn system, rather than all of one then all of the other is preferable when you have more than a couple of units (JRPGs which cap out at maybe 5 units per side can get away with all one then all the other, or simultaneous turn where you predefine your actions and they come out in an order defined by unit initiative, but beyond a few units the system would be unweildy).
Turn order is also an important prospect in Confrontation, your activation order has to be chosen before the round starts, so you actually have to think about which order you want to use your units in based on what the opponent might do, whether you win the initiative, etc.
Alkemy, by contrast, allows you to activate in any order, but units have Action Points (2, 3, or 4) which they need to spend to do things in their own turn and to react, so again there's a balance between being able to do your own stuff with your own activations or leaving the unit's AP in place so it can react.
I'd like to see that kind of system replicated in a TBS videogame, which so far have tended to be an all one then all the other, activate in any order type system. These are, of course, a different type of strategy, but one which I think is less interesting and more prone to imbalance as they tend towards a situation where you can identify the one most advantageous thing to do in your turn and then spend points to get it done, with little to no response from the other player.