Ships & Modules

I like Command ships, Love them for PvP or for the actual bonus they provide a good fleet. Astarte is a beast in the right situation.

BUT:
The T3 is so versatile and interchangeable. It can do your PvE and also work well for PvP doctrines.

Since you say you are not familiar with either, I'd go with the T3, and just do the learning curve with one ship for now. It can use covert cloaks for the travel in and out. It can tank as good as anything else, smaller than a carrier. It can be fit for some serious DPS application when needed.
I have to assume that someone in that WH knows what's going on. Listen to them, until they prove they don't.
Learn how to make enough ISK so that losses aren't a huge impact, and just get really good with what you do.

So T3s can fill pretty much any role, with just swapping out subsystems. Cloaky/Bubble Immune, Utility (webs, jams, neuts etc), RR, tanky, dps (short/long range), links... The list goes on.

Command Ships are bigger and slower, people know what to expect whenever they see one, has fewer but stronger link bonuses, does a few things well but also kinda locks you out of other things without switching to a completely different ship.

The utility in the T3s in very strong, but that is ofcourse based on you having the skills for all those roles to utilize them. Being able to mobile depot refit to something completely different is really strong, but you do loose skillpoints when you loose one. Their mass is lower so less impact on WHs also.

I can't tell which would be best for you, it all depends on the effect in the WH you want to settle in and what your friends can fly also. Since you seem pretty new to WH life I would think it wouldn't include cap escalations so don't need to worry about that yet.

It's hard for me to give specific advice. Tbh, I have never lived in a WH. I have camped them, and used them as short cuts across the galaxies.

I just think that the T3 is more versatile. Proteus can have amazing tank, or do good damage if you fit it for that.
If you have a good sized fleet AND reps to go with that, then other ships might be just as good.

Any Battle cruiser in your fleet can fit a link for you all. But a Command ship can fit multiple links. A T3 can also fit multiples.
A command ship can't do everything at once though. Tank, or Gank, or Links, you gotta kind of commit to one fit or another.

My suggestion about T3 is just a starting point. It doesn't meen you can't try other ships along the way.

Boosting ships are nice, but with a small group another active ship on grid is usually better than an inactive one off grid.

1)This is old math and may possibly be a little off. but the difference between a T3 and a command ship overall is pretty small especially if you consider the cost of a T3 +skill point loss on it's destruction and a Command ship. The biggest down side to the command ship is it is slower which is a pain if you are racing down a chain to pvp.

2) mostly any thing can run sites in wormholes. it will depend on how many people you have. but a few typhoons and a couple of logi was our cheap stake way of making isk in a c4. a C5 you should just invest in capitals and do the epic escalations (note, escalations may be going bye bye soon so this information may be a bad idea)

3) both would work. though once again how many do you consider a small group? will you have logi or local tanks? if you are unsure of pvp i would consider using Stratios or something completely different from a T3 or Command ship.

4) I choose an Eos because i like drones. ultimately it is personal taste and a bit on how you plan on fighting and what effect wormhole (if any) you are choosing to live in.