Jainus is the original server (Contains Torian, Syrephis, Marea, Silva, Ahkma, Tempest + Jin) this server has all the old overpowered stuff like epics, upgrades etc but IMO its not as big of an issue as it used to be.
Isen is the new (but not as active) server which has a "Crone based economy" but the server is not that popular especially now that the weapon/armor evolution system exists on Jainus. The two cool things about isen that jainus dont have is that you can buy armor stat spirit stones on the badge exchange store (badges are earned from Power Arena) and you can buy lvl 1 (10%) scrolls from an NPC ingame.
IMO you pick Jainus every time because its the more active server and players make up the game. There are many opportunities to farm and make RPs now that you should be able to buy an upgrade when the time comes. (Or depending on your class say FK that and buy an Opaniel weapon and transcend it.)