I don't get the argument the game is designed for 5v5 as a reason not to do 3v3. It's a different game mode , with different synergies , combinations and strategies. Adjust , adapt , embrace the change and let your skills get you wins.
There are some kits that reference 5 units , but so what , they are less effective in 3s just like omicrons are not effective in some modes. There are also some factions that dont have 5 units that synergize ; so should we not do 5v5 until they release another Tuskin ?No.
We also get to use more of our rosters in 3s, I personally love that aspect.
I love the breaking up of the same old teams week in week out, especially that first week of "how does this work again".
Also as another thought , the game is actually designed to have 6 units in a number of game modes , including fully playable units ie borrow a unit from ally battles. Maybe 6v6 could be a fun change to.
TLDR. 5v5 is one game mode , 3v3 is a different game mode. Play them different. Simple.