I seen threads asking if pvp will come, but none suggested how pvp ought to be in this game. I will give my personal opinion of how it ought to be. I will list my ideas from most important to least important.
#1. PvP definitely should be separate from the PvE "mode" of the game. In other words, your main island will be protected 24/7 and PvP happens in a separate world of islands.
#2. Resources ought to be separated from the two worlds, PvP and PvE. In other words, a lvl 50 player cannot send his resources from his main island (PvE island) to his PvP island. This way all levels have an equal chance, except players that buy gems will still have an advantage. However, players can send resources awarded from the PvP island to their main island, but not vice versa.
#3. In PvP there has to be a purpose in having it or an advantage in doing PvP, either for obtaining very rare resources, large sums of gems or coins, obtaining rare special (new) military units, event items, or all.
#4. This idea I copied from the PvP in goodgame empire from the higher levels. After about a month or season duration, the PvP islands will reset (similar to the test server, but for PvP mode only). I call it PvP Storm Islands because when PvP is over a storm (hurricane) will wipe all the buildings and resources from the PvP islands. Thus, you should send almost all of your resources from the PvP islands to your main island, especially your rare rewards. This way bugs and glitches won't be that much of an issue in PvP because the PvP mode will reset anyways. Also, this gives much more profit to The Settler's Online as it persuades players to buy gems in order to build their PvP islands faster (pay to win in pvp, but not permanent). Also, this makes PvP seem like an event and thus players will have to pick when to be very active in which season of PvP in order to obtain rare resources or rewards. Ultimately, the purpose of PvP Storm Islands is to get as much resources or rare rewards as possible before the next storm (hurricane) comes to wipe your entire PvP island away. Then you do it again and again in order to obtain rare resources for your main island paradise.
#5. Minimum level limit for PvP. This will persuade guilds to invest their resources on newbs for more buddies to form alliances with in PvP and thus become more successful in PvP.
#6. The ability to degrade other PvP islands by attacking them and looting them.