So here's the first tweak, which applies to Military Engineers and builders: the ability to clear artifacts, luxury resources, and strategic resources from tiles owned by the player. The appearance of certain "resources" (artifacts in particular) tends to ruin my city planning several times a game. Removing these features would allow the player to reclaim tiles that were vital to their plans.
The second tweak is to the Military Engineer. Their abilities are versatile, but their road-building function is all but pointless. Building a tile of road consumes one of their two charges, and since their speed is only 2, it takes an army of engineers and an enormous amount of time to build a useful road. This doesn't strike me as logical, since traders (which are available way earlier, offer loads of other benefits, and don't have a -4 gold upkeep cost) can build roads more quickly and for free.
My suggestion is increase the movement speed of the Engineer to 4, and remove the charge cost. This allows engineers to be used more strategically, and also fits the flavour of the Military Engineer (since Traders won't go to cities you're at war with, Military Engineers would be able to help your military by letting your units reach the front line faster). If this is too much of a buff, perhaps the Engineer could lose one of its two charges, since the unit would have more versatility.