This is going to be pretty much impossible past Lt. Commander. Using a Commander ship at Captain is relatively easy. Using a Lt. Commander level ship at Commander is insanely hard. It becomes virtually impossible to use a Lt. Commander ship at Captain, and I'm assuming trying to use a Lieutenant level ship at that level would be even worse.
You problem is basically Bridge Officers. At Tier 1 you get 3 BO abilities. At Tier 2 you get 5. At Tier 3 you get 8. That is a huge jump, you are nearly doubling the available abilities from Tier 1 to 2 and getting 50% more at Tier 3. At Tier 4 you get 10 BO abilities, which is only 25% more, but twice the number at Tier 2, and three times the number at Tier 1.
If you're already at Commander, I'm probably not telling you anything you don't already know, but I felt I had to start with a fair warning. That said, my experience so far is that you want to at least get as much healing as you possibly can out of those three BO slots. An EPtS in the Engineering slot and Science Team (or TSS) in the Sci slot is probably your only choice. You also want a second Engineering with Engineering Team so you can heal up your hull. Depending on the foe, you might have the Engineering and Science Team selected in combat, so you can repair hull damage, or you might need the extra shield heals and hope your hull holds out until you can use Engineering Team after the battle.
Your Tac officer you probably want using HYT, so you can finish off a foe quickly once his sheilds are down. Alternatively, you might go all beams and use either Beam Overload or Tactical Team. Cannons are also a viable alternative, particularly for the NX Escort, but all T1 ships can mount Dual Heavy Cannons. You'll have to go with Tactical Team, though, since CRF isn't available at Ensign.
I have found Covariant shields are the best, simply to keep me alive longer, and because I can use my BOs to regenerate them between battles. The same goes with hull. Strategically speaking, you're going to want to be patient. Do not engage the next enemy until you are completely healed up, take your time, and take on enemies one by one if you can.
Consoles, I just wing it. Obviously defensive/resistance/shield regenerating consoles are going to be a big help, especially on the TOS Connie, where you get two Engineering consoles. Also, good Devices are a huge help, the resistance thing from the Breen missions, and the fighters from The Vault can really help you out a lot. I'm guessing Borg or Aegis gear can help, but if you can even kill anything at all in a T1 at VA is something I don't know.
Honestly, I've been trying to do this, and it gets so frustrating I can't keep it up. Eventually I either switch to another ship (personally, the Connie refit isn't so bad as it bumps up my ability a LITTLE bit and keeps me with the same "flavor" as the original) or just play another Captain. If you can managed to get to VA, though, please, I'd love to hear that you did it.
I suppose I should add that if you can get a good team that doesn't mind you leeching off of them that's great, but I pretty much only ever solo, so that's not an option for me.
However, I have heard of folks who have gone all the way to Level 51 in a T1 ship, and without investing their skill points. They few who have done this all say what you have no doubt are experiencing: it's a tough climb. Still, best of luck to ya!
One thing I will add, after posting in another thread on the subject, is not to waste any skill points on Starship skills. Cruiser skill will (most likely) not apply to the T1 Connie, and obviously none of the higher skills will. Your best bet is to raise Starship Command as high as you can as soon as you can, and then move on. Raising your Efficiency and Maintenance Engineering levels so you have more power available may help compensate.
I ran all the way to RA 5 with my Miranda Tier-1. You have to do the hit and run method, Eng. Team 1, Science Team 1, High yield 1, Alot of Shields batteries and sometime a little help from someone else. I would say 75% of the game was by myself But long space battles. Dump all your weapons then run. it sucks but it works.Oh your not going to beat anything big like a cube or bigger thats where the help comes in. I still fly my Miranda as my Primary for PVE hopefully they will give her an upgrade to a saratoga variant which hopefully will be at least a tier 2 or 3.
I'm working on leveling my toon all the way to the top in a t1 tos connie. I'm already at commander 5, and realized that for this will be really tough, and I can use all the help I can get.
Can someone suggest boff power and console/equip layouts for me, for a tos connie, nx class enterprise, and oberth class, as I'm doing this with three different toons.
Hit me up in chat sometime mate, I use the Connie in the Btran Dailies alot- the Crimto fall beneath it (except for the Science Ships, they are a real pain). Im a Science Captain, and I use Beam Overload, Science team, and Emergency Power to Sheilds.
The Blue phasers fore and aft, and a photon torp. Purple Regen sheilds, basic combat XI engines, and a purple graviton deflector. even though i dont use them i would suggest some Scorpion Fighters, I use my photonic fleet.
I did lieutenant to captain in a Peregrine fighter. It wasn't so bad. I actually think the game is far more balanced when death is an actual possibility during regular play.
That said, here are some tactics that might help:
1. Hit and run: Go in, do as much damage as you can and when your shields are dropping or you're taking too much damage, pop evasive maneuvers and get out of weapons range to heal and wait for cool downs to reset. Then go back in for more damage.
2. Keep 'em separated: In some missions you'll come up against mixed npc encounters (a cruiser and a couple frigates for example). When this happens, pop evasive maneuvers and kite the faster ships out of range of the slower bigger ship. Then take them out and kite the cruiser around until you're ready to take it on.
3. Stick to a single facing: If you're blasting away at an enemy cruiser's port shield and they turn away from you, get back on that side as fast as you can. In a shuttle it's really easy to out-maneuver your larger targets, but escorts and science vessels can be a bit tricky. Use evasive maneuvers or an engine battery to get you where you need to go.
That said, playing in shuttle or T1 ship can be a ton of fun but it's not for those that don't like a challenge. The nice thing is that you'll save a lot of EC from not having so much to upgrade each time you rank up.