Fothal, before I start I wanted to say I agree I think this race is too powerful currently and needs some SLIGHT toning down. I just don't necessarily agree with some of your conclusions.
My conclusions:
[*]Wild Troll units are too cheap to create and the risk too low. So you loose one in four. So what? An army of wild trolls is unstoppable in the early game. Most of the problems with this could be countered by raising the cost to 100 gold each.
I disagree here, as Artic mentioned the REAL cost isn't the gold it is the Loss of a giant. Personally I HATE making wild trolls. I don't seem to lose 5% to barbarian, it is more like 80%. I almost NEVER have that promo wear off before they go barbarian. If they DO go barbarian, you then have to worry about said troll coming after you which them can reduce your forces even more.
Also isn't a hunter a 4/4 unit? Troll are actually weaker than hunter units which are not all that hard to crank out for other civs.
is 5 gold too cheap? maybe 100 is way too exspensive Although I would not mind paying more gold if instead of turning barbaian, they simply used the Enraged mechanic to be controlled by the AI (without the Enrages bonus) you just lose control of them till they win a fight. At 5 gold I wouldn't care if there was a 25% chance of that happening each turn until upgraded to troll hunters.
Or bump them down to 3/3

units and simply make them crazed until promoted to Troll hunters.
[*]The fact that units are not built with hammers means it is a little too easy to build buildings in cities. The smaller city size doesn't hinder this, it actually helps because most cities can reach the maximum size. Some of these cities are guaranteed to have a perfect balance of food and hills for maximum production output. Others are guaranteed to be perfect for commerce generation. The remainder help spawn Citizen units to expand the army.
It is slightly easier to build buildings early since you are only building cheap thralls, but that hurts late when you are try to use thralls for defense.
I have no idea how you see that it actually HELPS in any form. In no way is a 8 limit city EVERY going to compete with a 20-30 pop city for production if they were built in the same square. being a "perfect production -food balance means nothing... if anythign I make too MUCH food typically, I could support 2-4 specialists per with a 3x3 city with the giants easy. 1 or 2 farms, or 1 or 2 food resources are more than enough. I.m not sure what perfect commerce generation means but Commerce is commerce. More = better. Any city that makes more than it's maintenance cost is gravy.
Add to that you will have 2 or 3 giant city for each city a regular civ has, which means building 2-3 palisades, 2-3 libraries, 2-3 Parthenon... Any building that adds percentages basicaly cost you 2-3 times the hammers.
Flip side however is 2-3 market places, 2-3 elder councils actually help but still cost more hammers.
[*]Hidden Nationality on Wild Trolls and Hill Giants can be far too powerful. Crush entire civilizations without ever declaring war. Make civilizations defenseless against barbarians and/or demons by crushing their entire army with virtually no risk to your own civilization. Worse yet, the hidden nationality carries over as the unit upgrades. Just throw an army of Wild Trolls at your neighbors and eventually one will survive long enough to get lots of promotions (about 1 in 5 Wild Trolls if you start on this path immediately). That surviving troll (or later, Hill Giant) becomes a Juggernaut of Destruction with 500+ XP and is more or less unstoppable (eventually, most battles have 95% or better chance of success). 4-5 such "Juggernauts of Destruction" can wipe out anything with virtually no risk (60% or more withdraw chance!) I haven't even gotten to the final units on the upgrade path yet, but the mind boggles at what could be accomplished by 4 HN Titons and 4 HN Troll Elders, all with 300-500 XP. I like the hidden nationality promotion flavor-wise, but it simply isn't balanced. Or at least, it isn't for me.
THIS I agree with. The HN promo is HUGE on anything beyond Wild Trolls. I have not gotten a game to last long enough to get titans or elder trolls, speakers, or even Weilder of Arms for that matter. My HN hill giants, and Troll hunters are devastating my opponents before i ever declare war. Once every military unit of theirs is dead THEN I declare war and walk in with a army of thralls, using the HN units to wipe out any newly created defenders.
I stopped using this tactic because it was simply too effective.
My first inclination is to make it so that Hidden Nationality cannot be carried over when the unit upgrades. This makes a bit of sense to me conceptually. A Hill Giant with HN is fine. But when it upgrades to a Wielder of Arms, everyone with an ounce of common sense knows what nation it belongs to. It would still be possible to build up a few very powerful units, but only for a relatively short amount of time until opposing civilizations are able to realistically counter those units.
This makes sense to me. I think even HG with HN are very powerful, but anything beyond that is simply too much.
Another possibility is to remove the option to build Jotnar Settlers in cities, and make it impossible for the Jotnar to capture enemy cities (they are built on the wrong scale, after all). This would force using Citizens creation of cities and greatly reduce the number of "old" units.
If they rework the spawn rate as has been metioned, this may not be a good idea.
Not being able to capture enemy cites would be HUGELY game changing. I don't worry about too small buildings, some of the population is the people that lived there before (hence they can revolt) they stay in their tiny little homes
Modify the amount of time it takes for age-based promotions based on game speed. Part of the problem at "Epic" speed (which I typically use) is that the clash between civilizations doesn't start until at least turn 150, at which point you have a large pool of giants with 50+ years on them (1 age promotion) and several with 100+ (2 age promotions).
That doesn't scale based on game speed?
Make all military units "National" units with limits on the number that can be created. Unlimited Citizens, but no more than 8 Tier 1 units, 6 Tier2 units, 4 Tier3 units, and 2 Tier4 units. Then make Citizens upgradable to a "Militia" unit which is identical, except it has a defense strength of 8 (and still an attack strength of 2, or even attack of 0...and still no promotions allowed). The "Militia" would be the defenders of cities against barbarians, etc., and could be upgraded as slots become available for military units.
I like the milita idea, and having national unit limits wouldn't be too bad, but I think Troll hunters, and Hill Giants should be exempt from them, and personally I think your suggested numbers may be a little low but not a bad over all idea.
My next game I'm going to try a faster game speed. Perhaps if the enemy civilizations are obtaining technologies faster compared to how fast my army of Wild Trolls and Hill Giants are killing armies, the situation might not be quite as unbalanced.
My understanding is the AI does poorly on slower game speeds, you may see a differnce by playing at normal speed.