Other skills
I really see no other skills which are too weak... Forgery seems way too strong, to me (it is opposed by itself)! Disguise, Read Lips and Languages are less used because they are cross-class for almost everyone. Open them to Rangers and Bards (the ones they don't already have), and they'll get more use. I would open Innuendo to Fighters, maybe Spot and Listen, as well. Read Lips, of course, should be opened cross-class to everyone... Pity the poor Druid who goes deaf and can't learn to Read Lips! (I know a lot of hearing-impaired Lip-readers, and none of them are Rogues!)
Rope Use seems useful, to me, and my PCs take it, although I have to admit that they rarely take much, as most GMs don't seem to know much about knotlore or how to use it in game... Also, the DCs on most skills is 15 for a standard use, and that's a bit too high.
Yes, anyone can tie a rope to a tree. Roughly half of them, however, will tie a granny knot, instead of a square knot or a pair of half-hitches. When they begin climbing down, there are two things that can happen: Either the granny knot slips and binds (becoming hard to untie), or it slips and come loose... ("Aaaaaaagh!") With a good square knot, neither will happen.
There is also the braiding two shorter ropes together to become one longer one... It rarely comes up, but is indespensible, when it does.
Finally, look at a Boy Scout's Handbook, SAS Survival Guide, or US Army Survival Manual, sometime. There are ALWAYS large sections on tying knots. Read a little further, and you'll find how to use some timber-hitches to make a couple of long poles and some short cross braces into a ladder, or a travois, or even bend'em and form a sled. There are all sorts of survival shelters (leantos, teepees, etc.), as well.
Now I can certainly see adding Intuit Direction and Rope Use into Wilderness Lore and renaming it Survival, but then what of the Rogue? Rogues Use Ropes, too, but more for climbing... Five Ranks of Rope Use gives a +2 Synergy Bonus to Climb checks when using one. (In the 2e days, having Rope Use also gave a +2 bonus with the Lasso, a weapon missing from 3e!)
Rope Use, more than any other skill, is very dependent upon the GM running the game. Get an old Boy Scout, or an Army Ranger to run the game, and it will become very important!
Innuendo is also not a useless (or even less useful) skill... Once upon a time, in a 2300AD Sci-Fi game, I asked a character with Psychology to tell me when a certain NPC was lying... She detected a lie, and blurted out: "He's lying." The NPC was very upset with us!

Innuendo could have helped, there!
Likewise, I have seen Spec. Ops types use hand signals when sneaking up on opponents in the field. It prevents being overheard, allows giving directions and timing attacks from multiple directions, and otherwise coordinating men in the field. Rogues, of course, use it for "spamming flash", talking about their heists in public without giving themselves away even if overheard, silently passing signals, and recognizing each other in public, or getting into the Thieve's Guild HQ (just "fer instance").
Again, Disguise isn't that often used because Rogues (IIRC) are the only ones who can take it as a class skill (if Bards can't, they should be able to). There are plenty of times when the PCs will try to jump some guards and sneak into a fortress...
Some of the problem with skills, I think, stems from the magic system, too... Spells like
Jump, which (IIRC) gives +30, should not even exist. It cheapens the Rogue's abilities too much, and even the Monk's Leap of the Clouds pales beside this
First Level(?) spell. There are other similar instances, as well. (I have no real problems with magic granting ability, just granting so much, so soon, that it takes a 27th level PC with the skill maxed out, and they STILL can't compete (their jumping distance is still limited by their height)! Ah well... I don't know what can be done about that...
In any case, while the skill system could certainly be improved, there are no really useless skills. I think perhaps the best things that could be done would be to open up the Exclusive skills to at least two classes, each, and increase skill points all around. That way, with the max. ranks still the same, more skills and cross-class skills would be taken.
As for the Athletics skill, I have done something similar in another game, but it causes some problems... Balancing, Climbing, Jumping, Riding, Swimming, and Tumbling all fall into that category... Would Fighters get it? If so, that gives them access to Balance and Tumble, two skills they don't have, now. In 2300, I left Ride and Swim out, but that still leaves the question of what to do about Fighters and Jump... So, I don't think that'll get done.
Balance and Jump get used a lot, depending upon the campaign, terrain, and what the (N)PCs try to do... A chase across the rooftops will use both, as will a fight in the trees, or along the top of a bluff. Probably only a Rogue will ever take enough ranks to be able to walk a tight rope, though...
