The current server solution by Funcom is probably aimed to have one general server type. A 'base' server due to lack of better word, which is PVE in PVE zones in general and has got combat PVP happening in Agartha. That is what Funcom aimed at design wise from my take, at least the interviews and overviews indicate that so far. The factions living with a gentleman agreement, no open war above ground and fighting for Anima below in Agartha. Perhaps another server tagged 'RP preferred' or so, to indicate where role players could move to. But that is roughly the base they are thinking of I guess, closest to their game design.
As being a full term PVE role player myself I am quite fine with that, as I can ignore Agartha completely then and still could enjoy PVE in co-op play if allowed, or at least PVE without any disruptions or complications. There is no flag hindrance to complicate or even prevent grouping in PVE nor PVP zones then. Not sure if you would ask for a full fledged PVE server for yourself or if such a 'base' server would be alright for you. Opinions may differ certainly.
What the open world PVP players are asking for is either to change such a 'base' server type to allow for flagging or to have a separate server type with open PVP. With regards to that I am simply of the opinion that flagging will change the 'base' server type quite a bit (against the game design even among other things) and is therefore not the preferred solution across the board for me, but rather a new PVP server type then.
This is basically how Age of Conan is set up currently, PVE servers there have PVP opportunity in special zones only, PVP servers are open PVP everywhere except the main cities.