While I am enjoying the Mercs / hero and governor units, I think the fixed number of them at game start, independent of galaxy size or players, could be improved upon.
After some amount (half? 4?) of a tier of mercs are hired, make another row of 4 Mercs of the same tier available. This would allow players who got into the merc game late to still have some fresh choices, and make the merc game more interesting past the beginning of the game. I'd also hide Tier 3 mercs until Tier 2 was revealed.
Allow Merc upgrades to be purchased from the Bazaar. These upgrades would cost money and resources, but would allow an already purchased Tier 1 Merc to be boosted to a Tier 2 Merc and then a Tier 3 Merc. A few of these progressions are already in (+5 tier 1, +10 tier 2). Some Tier 1s are a little OP (too many moves or range, mostly) and this would reduce the gradient of some of them. Tier 2 upgrade package would, of course, only be unlocked once Tier 2 is onlocked. Should help offset the planned obsolescence or T1 mercs, and allow some of them to be nerfed a bit.