There isa reason an adept can't be as good at gun play as a soldier. The amount of training it takes to master your biotics is immense. Even vanguards only have rough training in gun play and mostly rely on biotics.
Just saying...
no there really isn't, Adept Shepard still gets cybernetic implants in ME2 (This isn't Shadow Run, we don't have essence), in the same game she can be upgraded to use one additional weapon of your choice. in ME3 Adept Cyborg Shepard can use any weapon in her arsenal. Training isn't something that needs to be cut off. There is no physical difference in terms of potential strength, endurance, sight, hearing, or ability to be cybernetically modified between any of the classes. The only reason the classes exist is to make an excuse as to why X power is under Y category. Shepard can even learn various skills despite her class from her squadmates such as Slam, AP Ammo, Warp Ammo, Inferno Grenades, Fortify, Geth Shield and so on. The New Protagonist is also a N7 grad, there is virtually no excuse for them not to be capable of the same thing and more since this is taking place in the future and undoubtedly technology and training has advanced again since Shepard's day.
As far as training goes Jack's has no training just experience and the will, that's generally all we are ever shown or told (Shepard did not have a Biotic Academy to study at either, which means she trained her biotics likely on her own or with another earlier biotic) and she can wield a freaking Shotgun and Pistol no problem the former generally being regulated to soldiers usually, Thane doesn't have 1000 years of experience but can use SMG's and Sniper Rifles, the later again being exclusive to Soldiers and Infiltrators. Samara can wield Assault Rifles and SMG's no problem but I will afford her hundreds of years as a Asari Justicar but even then she wasn't one her whole life and only did the training nearing the end of her time as a mother, and we are not playing the game from childhood on up, we cannot account for the training the protagonist will have prior to their N7 graduation and whatever time afterwards they have before we take control. Again we aren't playing as Padawan Luke Skywalker here, we are graduated and likely battle hardened N7 Marines, We've had the best training since the start of our military career, plus whatever experience on the field that entitles us to even have been admitted into the N7 Program, and whatever entitles us to be a Captain/Commander on this new expedition.
We have seen several "Classes" in multiplier that debunk the class restriction on abilities idea. The Volus are the best example of this. Suit's can be built to emulate all the various powers necessary while still allowing for various core power basic like being a biotic but still being able to cloak, (Volus and Asari Huntress), so no the Class idea is Stupid and should go the way of the Mass Relay... Colorful explosion throughout the Galaxy.
Basically they should build 4 skill hubs, label each as such, "Biotics" "Combat" "Tech" "Specialist"
The first three would house the obvious skills that fall under them, while the later would house unique skills that don't necessarily fit under the former three. Things like Weapon bonuses/passives, special passives that could effect one or several different abilities throughout all the trees, the special training passives that we saw in the various multiplayer classes (N7 Training, Asari Adept training and the like as examples, as well as where things like Special Ammo skills, and Health/Shield/Reputation/Leadership passives are.) and let the player choose and build what they want to be.