Wait, D6 has specialization dice? Hmm, I never noticed. Most D6 games I played, only the professional min/maxers took more than a single (or 2) specialization.
Warning, I think a spell of ramblin' is about to hit us. You have been warned!
That IS the root of the problem! It is not the game mechanics that are the problem. It is a player's lack of getting to use their character's skills/powers/etc. that is.
Are Desert Eagle .50 Calibres common enough in the setting that they would be useful in a Patent Law Courtroom? Are they common enough in a setting where the PC will get to use them enough to matter? If so, was this the setting that the GM implied the players would be partaking in?
If the GM said, "hey, lets play an A-Team like setting" and a player brings "Sherlock Homes" and then complains that he never gets to do stuff, who is at "fault"? If he brings "Murdock" and then complains there are not enough planes or other thinks that Murdock is good at, who is at "fault"? If the GM just says here is Game X, just make some characters and we will play, is it the players' fault that their character are not getting to do much that they spent their game mechanic exp equivalent on?
When a player presents a GM a character, he is giving the GM a contract. The contract says I want to play an adventure/campaign where this kind of character is important to the story. It is up to the GM to uphold their part in the contract if they accept the character. This means that all characters should get to do stuff, not just the "combat monsters" or the best min/maxer. Writing a campaign that makes Netskills all important but all the PCs are Street Samurai and Mages, most likely is an example of breaking the social contract between players & GM. Vice versa is an even better example, if they are are netters, why are they spending the whole adventure in meaningless gunfights?
If in an open skills based game, I expect challenges to match my character too. If I spend 5 dice in Law, I expect to need to lawyer or at least need to know about the law sometimes. We send Daniel Jackson into the Stargate because he has some useful knowledge skills, we do not send "Perry Mason" to go with him (except as an NPC that he has to deal with maybe). Maybe we now know the real reason Tasha Yar died, her player got tired of being a second string Worf.
If I spend points on disadvantages, I expect that they should be in play too. If I spend points on an NPC or pet or vehicle, I expect that it gets to be useful for most of the adventure. "Wait, I made a Smuggler for this Star Wars game and we spent the last four adventures stuck on Hoth, I want a refund on 25k credit disadvantage since I never get to use my ship!" "Man, I spent 25cp on a horse and all we have done is been stuck in caves, haunted houses and riding on boats!"
How much combat skills matter is more setting, players and GM than rules (true of any other skills too, of course) unless the game is basically a combat sim. I can not count the number of times I have heard people whine because they "had" to play the cleric or other utility class in old school D&D. I was always, "WHY did you have to?" Most responses are something like, "we would die without a healer" or other such lame excuses. Then let them die and maybe they can learn to play the cleric if it is that important.
Ramble, ramble, ramble. Did someone notice I have spent points on the "Rambles" disadvantage? At least my girlfriend likes it when I ramble.
It also sounds like you have something of dominate player syndrome or skilled min/maxer issues (or issues with underskilled min/maxers as the case might be), probably both. Neither of these are issues with the rules themselves either.
Oh, wait, there is a real topic, I would suggest making an optional rules section, toss specializations there and then let people who want to use them deal with them or not.