Tutorial

Playing the tutorial will only go so far to explain how to play the game, even though you will still get the occasional tip pop up after you've finished it, but it doesn't tell you everything.

One thing you are told about, but may miss is; you can set your skills to auto execute. This is done by holding down the buttons shown in the bottom right hand corner of the screen, move your left thumbstick to highlight a skill, then press R1 (or RB) to make it auto executable. Most powers will have different auto settings so try different ones out for yourself. You can also set specific skills as quick access powers by highlighting a skill, then pressing in L3.

If you have created a Romulan character, as recommended, your base will be the Romulan Flotilla, but, you need to unlock the Romulan Command Centre so you can claim the promotions you will get whilst levelling up. In order to do this, you need to complete the missions The Search For New Romulus and Turning Point. Also, once you complete those missions, you will be able to choose whether to join the Federation or the Klingon Empire, which will then let you play with other players from those factions.

Skills

Each time you level up, you will gain a skill point you can add to your skill tree. Like any MMO, the only guidance you'll get from the game is a short description of each skill.
I've put together some skill trees which beginners should find useful. All these links below are a balance of health/healing, resistance and damage output for multiple play styles and ships. They also include, recommended gear from missions and reputation with a few other recommended items that can be purchased from the exchange but they do not include weapons sets (that’s for later). They are here as a guide for new inexperienced and novice players and have all been tested in various advanced PvE queues and at low level.
(Caveat: some advanced PvE's can be quite hard for experienced players, these skill trees and recommended equipment will not make you invincible!)

Bridge Officers

Bridge officers are awarded by completing the first few missions and at levels 5, 8, 11, 15, 25, 35, 45, and 55.

Another thing STO doesn't explain properly is Bridge Officer (BOFFs) abilities. Bridge officers come with a set of default abilities which can be changed by purchasing training manuals from the bridge officer trainer and on the exchange. There are quite a few to choose from, especially when you get to end-game.
The main ones you need to know about, which are the ones that will help keep you alive, are Engineering Team, Auxiliary Power to the Structural Integrity Field and Hazard Emitters. Tactical Team and Science Team will also help keep your shield up and also remove debuffs and Reverse Shield Polarity will make you immune from energy weapons for a short time and regenerate your shields. You can set all these to auto execute.

More information on bridge officer abilities can be found here;
https://sto.gamepedia.com/Bridge_offi...

Bridge officers of different races also come with specialist traits for both space and ground, such as additional hull regen, crit chance, etc.

As a Romulan, you should be looking out for very rare quality (purple) Romulan bridge officers with the Superior Romulan Operative trait. Other lesser quality Romulan bridge officers are ok, if they have the Romulan Operative trait, but you should upgrade your bridge officers as soon as you can.

Jem'Hadar Vanguard characters just need to use the Jem'Hadar Vanguard Bridge Officers included in the pack from the C-Store, although you are only limited to one science, one engineer and one tactical officer. You also may purchase a Superior Romulan Operative from the Fleet Embassy.

More information on bridge officer traits can be found here;
https://sto.gamepedia.com/Bridge_Officer_traits

After skipping through the mission journal, there are a number of recommended missions you should do which will help build your character and prepare it for end game. These missions, which you can play through early on at low level, will award you with gear that will increase your resiliency, damage output and overall effectiveness in TFO's, on both ground and in space.

A full list of recommended missions can be found here;
http://www.lethalitysto.com/mission-rewards/recommended-mission-rewards/

Duty Officers

At level 11, you will unlock Duty Officers (DOFFs). At first, you will only use these to send off on missions. Those missions will gain you experience while you're off doing other things to help you level up a little faster. I suggest you set off as many Dilithium missions as you can, then set off the Skill Points missions, then just set off what ever you can. Levelling up your duty officer commendations (ranks) will earn you extra rewards/bonuses in-game, more information on these can be found here; https://sto.gamepedia.com/Commendation
When you level up a little further, you'll gain better duty officers which you'll be able to use to buff your skills, but more about that later.

More information on Duty Officers can be found here;
https://sto.gamepedia.com/Duty_officer

Research & Development (Crafting)

At level 15, you will unlock Research & Development, but, you will be able to start collecting materials used in R&D straight away. Keep your eye out for these materials whilst doing missions and collect as much as you can. R&D materials are also given out as rewards for completing PvE Task Force Operations (PvE queues).

Because of a bug on console, you can unlock extra R&D slots really quick by slotting the Research Project - Science Technology project. This will gain XP for Science, Officer Training and Special Projects. This does not work on PC because Officer Training and Special Projects don't level up.

After getting your science R&D school to level 5 and unlocking four project slots, I suggest running as many Research Project - Kits and Modules projects as you can (3 max), each day, to get your Kits and Modules to level 5. This will unlock the ability to make large hypos and large shield charges which you can use to heal yourself on ground maps.
After that I recommend running as many Research Project - Engineering Technology projects as you can to get your Engineering to level 10. This will give you the ability to start making hull patches which will help heal you in space.
When you have got Kits and Modules to level 5 and Engineering to level 10, carry on running as many Research Project - Engineering Technology projects as you can to get your Engineering to level 15. This will finish unlocking all your R&D slots, except for the bottom one which you'll have to unlock at your fleet research lab, and you will also get the personal space trait Give Your All.
After that, I would personally go for getting Kits and Modules to level 15 to unlock the Technophile trait, which is a really good personal ground trait that will increase your kit performance. You can check out the link below for other traits and decide for yourself where to go from there.

Getting each R&D school to level 15 will earn you a personal trait. Details about those traits are listed on the wiki using the link below.

More information about Research & Development can be found here;
https://sto.gamepedia.com/Research_and_Development

Lethality

Star Trek Online Fleet

Creating Your Character

The Tutorial

Advice For Beginners

Skills

Bridge Officers

Skipping Missions

Recommended Missions

Duty Officers

Research & Development (Crafting)