Here are my ideas for 2.4.3
GEAR:
As you said, d3/ heroic gear would be a great start for main gear. However, do not allow people to buy the Shield from Bt as you could on TMV. That had led to many boss kills with shield drops, and 20 pissed off people in popes finger. the other 5 were loling. Same goes for trinkets/belt/rings/boots/wrists/cape/neck. Also, since i know it probably is still near impossible, Somehow make the Chess Event loot avaliable pre Tk/SSC. Either vote tokens,oc, Donate, or some other method. This way tanks can get their hands on their buddy King's Defender, and healers the shield, and so on with other classes.
PROFFS: Good how they were on TMV, but if possible, make it so people cannot do the wep smith/armor smith bug, or dont have the weapons on vendor. Do not sell the Blue patterns from Kara/Za, make people obtain them Via the instance, could also do same with epic/blue crafting reagents such as Primal Might, and nether.
Mall: If possible, the server should be a PVE server, so people will not flag in a mall, with that, there would be no need for some to flyhack to the other mall to pwn new players, eliminating the mall hackers, or at least ruining their fun. Another option is to have a combined mall.
Raids:Grouping.
Assuming the population will have a slow, but steady grow, at first, to cater to the player base, cross faction grouping would be useful, just to allow for them members to be able to do more than Kara at first. once the player base this could be dropped, or continued. No lockout timers, this fucked over our raids on TMV, and ruined the fun of raiding on a private server. If you want to do one raid, fail, and wait 5 days to do it again, play retail. There is no need for lockout timers. and of course, no custom bosses :/
Vote Items: Donation Items: Do not make it PVP gear, make it possibly high end PVE gear, that is hard to obtain: IE Cataclysm's edge/Bullwark Of Azzinoth/ Apylon: etc. The items being PVE will truly benifit the players alot more than gladiator gear would. If PVP gear seems to be a high demand, have functioning Arena/BG for it.
PVP: Its a PVE server. Possibly have Functioning Arena/WSG to que when its at least 1v1 and so on, allowing people to pass the time between raids and potty time. Have PVP gear be at a cheaper cost. But again, its a PVE server, should be mainly focused towards PVE.
Events: Have events with PVE rewards, same concept as Vote items, but maybe not as powerful items. Possibly items from yet to be released content.
GMS and RAIDs: Do not allow gms to raid with character's they have the power to .add item. Is it nice? yes, but it takes the fun of raiding out when you know your tank will not die, or your healler will not go oom, etc. If a GM wants to raid, they should have a player acct, and GM account.
That should cover all the points i have off the top of my head. Feel free to call me a bitch and whatever, but those were some of the problems/benifits with TMV that i saw, so i put them all ina nut shell