Well, I was thinking about creating a Ukraine mod, before even checking out this post, and here are some of my thoughts:
Leader: Sirko was more of a field commander - a legendary general, granted, but not a politician by any means. If sticking to the Hetmanate period, I would strongly suggest Ivan Mazepa - he reigned a long time, and was a great diplomat and politician, heavily subsidizing arts and culture, and bringing order to Ukrainian economy.
UU: Zaporozhian Cossack seems fair enough, but there's a clash with Russia's cossacks ( Even though historically, Russian cossacks evolved from the phenomenon of Zaporozhian cossacks. )
My suggestions are: Chajka (replaces trimere or galley, is cheaper, can enter land tiles that have a river next to them, bonus against other naval units)
or
Mobile Camp (strong gunpowder/artillery unit, replaces musketman, extra movement on open terrain, heals +1 per turn regardless of action taken, only weak to artillery, bonus fighting infantry and cavalry)
UB: I thought of Sich straight away, but envisioned it more of a tile improvement. Replaces fort, can only be built in a tile next to a river, can't build more of them than the total number of cities the Civ controls, grants all defensive bonuses of the fort but also massive food and moderate production boosts. Also optionally, once every so many turns produces a Ukrainian UU.
UA: "Children of the steppes" or "No end to Cossack bloodline".
Horse, Fish and Wheat resources times two,
and if "Children of the steppe", then all units receive shock 2, drill 1, and some other (maybe random) elite promotion, e.g. sentry, amphibious, logistics or something like that.
if "No end to Cossack bloodline", then bonus fighting in friendly territory, and negates any bonuses enemy units might have for fighting in their territory (e.g. neutralises any combat bonuses from social policies and wonders).
Another idea is settler production speed reduced by 50% (Cossacks did tame new lands like there was no tomorrow).
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As a totally unrelated idea, I think a wealth of historic research available today merits the creation of another Ukrainian civ - UNR (Ukrainian National Republic) 1917-1922. Leader: Simon Petlyura or Pavlo Skoropadksiy. For those who understand Ukrainian, a wealth of info here:
http://unknownwar.info/
For those who don't - UNR existed briefly during the Russian civil war, and fought a bloody campaign against the Soviets for over 5 years.
UU: mounted machine gun (machine gun cavalry, as in Makhno's army)
UA: "Peasants turned Patriots" can draft units at the cost of food and growth
National Wonder: First Winter Campaign (wounded units fight as though at full strength, friendly units get spawned in enemy-occupied territories)
or
"Holodniy Yar" provides similar military bonuses, but also gives the city massive defensive bonuses.
This second idea is just a thought, yet to be matured. But the wealth of various weapons, tactics and military innovation during that war warrants maybe a creation of an entirely separate strategy game, it's fertile enough to create a separate gaming world in it's own right.