Some of the lower level zen store ships come with better bridge officer layouts. Look at the Rhode Island compared to the tier two ship. The Rhode Island has two lt spots where the tier two science ship has only one. But as far as end game it all comes down to bridge officer layout and the console.
and found that the refit only had an extra console for about ?4 :S
Not really seeing this. The time ship is a better science ship, the bugs are better escorts, and some would argue that the mirror universe enterprise E works the best as a cruiser and these are all purchasable via energy credits right now.
Also, looked at the list twice and it might be that it's 6:35 AM here but I didn't see the mirror universe cruiser on the list or the MUscience ships on the list but I own one of each.
Anyway. It's really dependant on how you setup your ship and right now there seems to be this cookie cutter blend going on because they've limited beams damage the way they have. So I'd really suggest you get a ship that has cannon capability really I would because you won't be disappointed.
Here is the thing. The Zen ship are marginally better, but only by a small margin. They might have slightly boosted stats and the unique console, but they don't make or break a game.
I wouldn't worry about getting a Zen ship until you are at level cap anyways, as you age out of your leveling ships too quickly to be of much practical use. Some of the consoles might be useful later on, such as the Emission-Seeking Torpedo on the Consitution class Refit but the ship itself is just... kinda cooler than normal.
Even then, keep in mind that you can completely be competitive in your RA level ship in endgame content. Also that if you want any of these ships, you can buy the lockbox ships off the exchange for (several hundred million) EC. And the Zen you can get for free by grinding out dilithium and trading it for Zen on the Dil exchange. So do not feel pressured into buying an ship, and don't feel pressured into cracking open your wallet.
The big advantage of Zen ships is that free ships are very straightforward in their BOFF layouts, while the Zen ships let you do some more-exotic officer layouts like an escort throwing out warp plasma (Armitage) or a cruiser with attack pattern omega (Regent, Excelsior). Add to that the extra console, which usually are pretty gimmicky and at admiral levels are limited to particular ships anyways. With only a few exceptions though (the 3-pack ships mostly), Zen ships have the same 9 consoles, 12 boff slots, and hull/shields/weapons as their free counterparts. As such a freebie Patrol Escort is just as dangerous (in some cases more, in others less) as a $25 MVAE.
You buy a Zen ship because it does something cool or because you want something different, not because its 'better.'