The "Event" What-if counters like SNAFU, Extra Strategic movement counters, V2 Rockets etc. Should be the easiest to add as they use the same basic mechanics as other "real counters" in the game.
The Alternate unit counters would behave just like current Game ones (what-if AC and Naval markers etc.) the real trick here is to get their "entry times" correct if used. That I think would be the larger issue.
The only counters - Nukes and Extra Factory counters aren't simulated by anything currently in game (unless you have programed the Soviet vs West Scenario completely - that oneScenario "breaks" several "rules")
The Strict Neutrality markers would be nice to use but I understand we may have them become an official Rules alternative/change in the future.
For me the Extra Strategic Move counters and the "SNAFU" counters would be the ones I would want to see soonest.
The Last Stand Rule IMO - should be modified to only include countries with "Factory count markers" (Fr, IT, GE, UK, USSR) otherwise you could have some minors lasting way longer than they should. In reality I think the only actual example of the rule might have been Stalingrad and Berlin in the actual history.