If you haven't played SS before, I would HEAVILY suggest playing vanilla as the game can overwhelm new players
Seconded, Vanilla first then mods later. Get accustomed with the basic gameplay since mods tend to throw alot of stuff at the player.
Quick warning on some mods:
Nexerelin - Has a "Vengeance fleet" mechanic (originally from another mod). If you are on bad terms with another faction, get ready to be hunted...alot.
GraphicsLib- Might cause some problems on low-mid PCs, you might want to check the troubleshooting guide in the mod just in case.
LazyLib - If you want to play with mods, you will need this. A large chunk of mods requires it.
Dynasector - Gives everyone unique ship variants. If you have this, don't be surprised if you see pirates with really good weapons.
For factions:
Diable avionics - the faction itself is on bad terms with the Vanilla factions and on neutral terms with the pirates. Visiting their bases will put you in risk of some pirate attacks.
Templars - If you feel like you are invincible, try taking these guys on. Though to be honest, they are pretty strong.
Underworld - has high-tech
pirates bandits space jews I mean..."tax collectors" that will ask you for some stuff. Give them nothing, then you get yourself a fight. The mod also adds new ships for the pirates which makes them challenging to fight.
Red- They are a hostile faction with units that you can find in a SHMUP game. You can say they are near dangerous as the templars.