If you think that Cybran is only relevant on maps where frigates are relevant then ...
Anyways, back to the topic : Cybran frigate is the best and it's intended that way, they have weak t2 stage, no hover, their t3 is ok, low hp Mexes. UEF on the other hand has weak t1 navy stage, ok t2 stage with destro that's good if micro'ed and an amazing cruiser (It can get though a shit ton of TMD's compared to Sera one) + shield boat which basically defeats any potential for enemy to use torp bombers (This is a huuuge advantage). Their t3 navy is the best with BC destroying all destroyers with ease and loosing only to Aeon t3 battlships. And these are just the things considering only navy.
Let's take a look at a classic t1 navy spam map : Roanoke
What advantages does UEF have over Cybran? Better intie, better arty for drops (6 lobo's 1 shot Cybran t2 pgen/t2 mex) while medusa are the worst arties for drops. They have a gunships that can drop units around which allows you to re - take small islands in the mid game, they have equal or better t2 navy depending on map (how much dmg can UEF cruiser do) and better t3 navy especially in early t3 stage with their BC's. You have Janus to kill all of enemies BP in the base once you win air (They are also equaly strong as corsairs vs big structures like Pgens and factories if micro'ed correctly). They also have access to TML on ACU which is an amazing upgrade for this map.
Cybran : Better frigate, wagners, corsairs, torpedo + stealth ACU, Stealth boats + nice t2 navy with stealth combo forcing 5 mass/ s scout stream in the mid game.
On another note I did some number crunching and testing to see how strong Cybran frigate really is compared to others. In order to equalize the difference as UEF you need to get 16 frigates for every 15 that Cybran has. In The early - mid game that means assisting with 2-3 more engies which drains 2.5-3.75 mass/ sec which means you need to have 2 more mexes then your opponent which you should be able to achieve with better inties by grabbing more small islands.
Such "imbalances" such as these only matter if you play exactly the same as your opponent, don't use any of the other available strategies and don't use other of your Faction's advantages. Not to even mention the fact that due bad eco control most games have significant difference in total mass of players. Much larger then the 350 mass advantage for Cybran in the early navy stage (7 cybran frigates vs 7.5 UEF frigates).