1). Largely underpowered unless you can easily get Critical Hits, which may force a player who wants to run-and-gun to instead be sneaky
2). HUGE lack of mods (not to be confused with the PC modding community), and out of the six weapons that have them only two can get more than one modification
3). For the more sneak-based players, no Energy Weapon can (for obvious reasons) use a silencer/suppressor
4). While they do have very varied effects, there isn't as much variety (as said in an often-occurring load screen), which can turn away those who get bored easily with each individual weapon and thusly crave many different weapons to use
5). Funding the use and repair of said weapons can be costly, especially for the hoarding types (I'm included in this little sub-group :disguise:)
6). In later levels, there are few EWs that can compare to the devastation of heavy-hitting Guns like the .50 cal. and Grenade MG
7). Ammunition is less common, and there is no AP ammunition
8). Said weapons are hard to find in the game world, as not many enemies use them (the ones that do are often NOT to be trifled with) which, again, is a down side for hoarders
9). I could go on, and on...and ooooooon, but I'm tired of typing
NOTE: As I've noticed in this thread, I'm not the only one with these opinions. However, I am not biased towards EWs in any way (I LOVE the Laser RCW and the Gauss Rifle), but I am not without disgruntled complaints.
