There are a lot of good mods that go well with EEM. It all depends on what you want to do really. Aesthetic mods that add better visuals (such as new skybox, small grid versions of large grid blocks, things like that), are always a good bet. Shields are fun (sometimes i feel even required to stop stupid stuff from doing crazy damage, like bumping a rock while mining), but they can quickly overpower you compared to the vanilla approach of EEM. Nanites take a lot of the tedium out of the game (welding, parts carrying), but none of the approaches on the market right now are even remotely balanced (and one is incompatible with EEM).

As for the best way to start, if you're not going to craft your own solar system, I prefer the vanilla solar system start with an EEM space miner as my respawn craft. Keep in mind that EEM is space based, so if you're doing planet content, we won't be joining the party down there.

I know im late, but as he said Shields, but I would also recommend adding in Corruption and Reavers by Merdius IX / Lucas. Mexpex Weapons would help with firepower and Nanobot Build and Repair is a must have and I cannot recommend it enough. As for quality of life in this worldspace I would also recommend Easy inventory(once you use it you will never take it off)