Can be considered a con, as Maven is not a very nice lady in the least.
Depending on your alliances this may very well be to your advantage though (well, not really, as it has no effect what so ever, but for RP purposes). If you're in the Thieves Guild having your patron in charge on the city your headquarter is in would be a huge victory - granted she runs the city already, but it's nice to have it on paper.
But if you're a good guy, this might not be too good. However if you're joining the Stormcloaks Markarth gets sacrifaced to corruption as well. Riften is a lost cause(within the game), Markarth can be protected.
As for the OP's question very little changes. If you join the empire 4 Jarl's are changed, if you join the Stormcloaks4 Jarl's are changed. At the end of both storylines you will fight and kill the leaders of the opposing army. Whiterun will be damaged no matter which side you join. Joining the empire will cause harm to Windhelm, joining the SCs will cause harm to Solitude - however both cities will still be fully operational. None of the camps on either side will be affected by the war, though you can clean out everyone but the commander on all.
The only true change is, as some have stated, that the thalmor will more or less be thrown out of Skyrim - oddly enough their embassy+torture castle are in no way affected by this. I actually think having the Thalmor around is a big plus, as it's so much fun killing them.
Save Maven(depending on player's affiliations) I'd say all the imperial Jarl's/governments are superior to their stormcloak counterparts:
Original - Replacement:Dawnstar - Skald (stormcloak, just an old geezer, decent enough Jarl I suppose) - Brina (imperial, ex-legionnaire, a strong Jarl, with a realistic view of current events)
Falkreath - Siddgeir (imperial, spoiled brat who doesn't do anything for his people, however he let's his very competent steward take care of affairs) - Dengeir (stormcloak, ultra-paranoid elderly man who distrusts everyone in the hold)
Markarth - Igmund (imperial, a strong and competent Jarl though nothing too spectacular) - Thonar (stormcloak, corrupt ass who wants his family to own and rule the entirely of the reach)
Morthal - Idgrod (imperial - though impartial to who wins the war, however she does seem to play it up to the Thalmor, attending their parties, etc. Seemingly slighly crazy and eccentric, but it would seem her "gift" is true) - Sorli (stormcloak, this one might be better depending on your views, she seems competent enough - though she is utterly flavorless)
Riften - Layla (stormcloak, lazy and stupid, does everything Maven says) - Maven (imperial, corrupt ass, but in charge no matter what)
Whiterun - Balgruuf (imperial, competent and independent, even allows open Talos worship in his city) - Vignar (stormcloak, perfectly ok Jarl, if not a bit too old and lacking in experience)
Windhelm - Ulfric (stormcloak, strong Jarl but seemingly ignoring the rights and well-being/protection of everyone who isn't a nord) - Brunwulf (imperial, also a strong jarl, a war hero with a realistic and unfavorable view of war, wants to rid Windhelm of racism)
Winterhold - Korir (stormcloak, paranoid and spreads hatred and intolerance of magic/ the college) - Kraldar (imperial, tries to remove the fear of the college)