Getting upgraded weapons, shields, and engines has some definite plusses here. I have gotten them from blowing up PvE ships and as rewards for completing missions; BUT, that's not always the case...at least with any consistency.
My Science Vessel received more than enough of these finds and gifts to upgrade without much difficulty within it's own tier; however, at Tier 2, when I went looking for upgrades using EC's, the best I could find were at SB 39. There, you can only buy MKIII Phasers, Photon Torpedos, and Photon mines. Nothing MKIV at SB39, Earth Space Dock, or Memory Alpha for EC's
For a Science Vessel, I don't consider that much of a big deal...not really; however, for my Escort, I find this to be a very big deal. At Tier II, I cannot use EC's to buy MKIII or MKIV Cannons, Photon Torpedoes, Quantum Torpedoes, or Plasma Weapons of any kind.
What's worse is for whatever reason, most of my mission rewards were tactical kits and body armor...no shields and no weapons (did get an engine). By promotion to Tier 2, after upgrading all stuff for my away missions and selling space weapons from my old ship, I only had enough EC's left to buy a dual phaser array.
So...here's my Tier 2 loadout for weapons:
MK II Dual Phaser Array
MK II Dual Heavy Cannon Disruptor Array (never had any more than 1 of these)
MK II Photon Torpedo Launcher
MKII Disruptor Beam Array
The engines and shields are both MKII standard.
I am short of EC's, but even if I had enough, I would not be able to get cannons at all, nor turrets. That leaves one option...Badges of Exploration 2. Lots of runs through the Hromi Cluster...Oh wait, that mission isn't open to my Lt. Cdr 1 yet. Why is that?
Considering Klingons can buy the most advanced Vanilla weapons as soon as they tier up, why should it be different for Feds? It definitely puts me at a disadvantage all around, especially since I don't even have the avenue to earn what I need to buy what I need right away.