Here is my thinking behind your issues. Please feel free to poke holes in the logic, because if it is flawed, I will change it. This is merely to convey the purpose behind them:
Re Mohawk Sentry:
This is designed to be a unique unit like the fast worker. It is not designed to gain you power in the conventional sense. Instead you have the ability to scope out anyone anytime, so long you are not in declared war. It is virutually a spy immune from getting caught, it's reason for not being able to upgrade is so that you may build it up until the end game and be able to keep survailance on rival SoDs at all times with impunity, an ability no other civilization has.
I am aware of the issues with start as minors. I see two solutions to this. The first would be to make it invisible as a covert unit, like special forces, but this brings along with it many issues. The issues are numerous and suffice it to say it would take significant SDK modding to get around, too much for me to consider viable. The second idea I think I will implement is to give the Sentry a +100% defense against Warriors. How does this sound?
Re Scout can attack:
This is just simply to make the early game more interesting, and to put the human at the same disadvantage as the AI has in defending against worker steals. Yep you need to defend your workers. And in old ancient times empires couldn't just send off massive work parties to build roads without military escorts either. Of course gameplay trumps realism, but in this context, the fact it forces humans to defend workers just like the AI has to seems like an improvement in balance.
I have played a bit more scouting around with the Mohawk Sentry. It usually ends with a few "must" and a few proper game issues.
1) Micromanagement is now enforced on it. On auto-scout it simply kill himself parking on a flatland near an enemy city/warrior/barbarian. The problem here is that the game pathfinding algorithm, amen to that.
2)Both him and my workers usually die when I gave them an order and then soon thereafter an 1-square-a-turn-enemy move nearby. Sometimes they stop working and give me the control back, sometimes they continue as nothing happened - and die horribly. Never understood why this happens only sometimes.
3) It is estremelly powerful and well thought, it is probably the only scout that I never built out of the starting one.
4) For the civpedia it upgrades to explorer or special force, but in the industrial era I can upgrade it to cavalry [800 gold, LoR_Light]. It is normal or something went wrong? [No, I dind't put any marmalade in the xml files
]
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In the end I think the Mohawk Sentry is quite good as it is now. My problems with it were from a willing design that you explained, and once one start to be used to it and look at it as a precise choice from the developers it works fine.
I have some other feedbacks that gave me some thought.
First: the rev sistem make oversea cities a pain unless you give them heavy garrisoning. This is usually not a true problem, but on some maps [arcipelago, terra-like or islands] it make almost impossible to keep them. Do mind, I'm not speaking of oceanic colonies [which I feel is normal] but extremelly nearby ones, like Crete or Sicily or Ireland. I feel the problem lies in the standard-bts colony system, which react in the same way. Of course I don't think it is a needed change, but if you have some info on "how" it works overall the sistem it might be usefull. Simply building stuff to keep them quiet sometimes works and sometimes increase the "colony" penality. Sometimes I have a colony penality to a 2-coast distance from my capital, sometimes none on a fartest continent. And nor Versailles or forbidden Palace help with that. It is possible to make those wonders to work as "capitals"? Thus making such tactical decisions... undestandable?
Second: I really like the new steamships and use them often. But I also feel that there are a bit too much of them, it feels... crowded. Usually one end building a lot of stuff that need istant upgrade to the next model. True, it is historically accurate, but gamewise it annoying. Maibe it could be viable to remove a couple of them? The problem begun with Ships of the Line [which one almost never use, along with the ironclad gunboat] and end right before the modern ships [destroyer, battleship]. In-between of them there are a lot of "patchwork fleets"...
Third: submarines. I don't know in multiplayer, but I almost never find them useful in single. Am I wrong or it is a common problem? Also, It's really nice to have scout planes on sea, or some kind of air superiority, but in the end modern fleets are built around battleships... instead of carriers. Most fleets are built only of battleships and destroyers. True, only a few years ago the americans whould have killed for a nice battleship in the arabian gulf for inland bombardment, but for more than 50 years the war at sea was fought... in the air. In civ this never happens. Carriers are a waste of time for the most part - just build destroyers and you're safe from those weak and pesky planes that pose no real treath to your ships. Of course the "very modern" sea wars are accurate once again. Miss'le the enemy to his doom and you're sound and safe.
Fourth and not an actual gameplay thought but a request: in some mods [TAM, for example] there is a desert-promotion that work like wood and hill ones. Usually there are not a lot of deserts in a random game, but in the world replicas there is a LOT of desert. It will be nice to have special troop promotions that works on it. This might be extended to the ice - there is not a lot of tundra and ice usually, but a ice-tundra promotion might be useful on Arboria games or cold settings, let alone man-made scenarios. It will be hard to implement such promotions? [I'm not actually able to do that alone. I can tamper with actual promotions but when it comes to new ones all crash in multiples "somewhere" and no matter how hard I try to fix it it only worsen.]