In short, yes, they got the shaft. And it sucks. One of my mains was a Joined Trill...
Then you haven't understood the new skill system yet.
1) There are less skills now.
Just from that list - Trills used to get +3.3 to Starship Energy Weapons and Starship Projectile Weapons. Now they get 3.3 to Starship Weapons. There is no longer a distinction between these two skills! They still have about the same net effect - your skills with all weapons goes up by about 3.3 (if it wasn't for the next point, which shows you that this 3.3 is actually more in effect than it used to be.)
2) The modifiers are listed now lower than before (technically, the effect is still pretty much the same).
Most BO skills in the old system now on Holodeck were affected by 3 skills, one Tier 1, one Tier 2 and one Tier 3, 4 or 5. If you added the total of all 3, you got the max effect at roundabout +100 skill total.
Now, you get about the same with a total of +33 from just a single skill maxed out. So the +3.3 actually represents about 3 times more than it used to.
(Scary Math Caveat: It may be that the total value generated by these skills is only 75 % of what was possible on Holodeck. In that case, it's 3.3 x 0.75 = 2.475 times what it used to be. But I don't want to scare anyone with math here. Halloween is over and we don't celebrate it anyway in Germany.)
A lot has changed under the hood. (It still doesn't explain why Engineering Consoles grant only half the energy level bonus they used to, though, same for EPS Flow Regulators loss in value).
Joined Trill was a hot mess before the skill revamp. It's a bunch of tiny numbers in random places making no overall important effect. The Symbiote (should be Symbiont in the first place) trait is in desperate need of a buff.