This is going to be fairly lengthy and I'll just try and break this down into Pros and Cons for both :
Energy Weapon Pros :Generally more accurate
Lightweight
Low strength requirements
Only three types (plus variants) of ammunition, all of which are interchangeable with Science skills. Not counting Flamer Fuel.
All ammunition has degrees of armor penetration
Recharger Pistol and it's unique variant in GRA allows you to have a quality sidearm with no ammunition requirement later on in the game.
Energy Weapon Cons :Not a whole lot of variety so get used to looking at the same three weapons for a long time
Struggle when the "tier up" period occurs, this is when you start to see different breeds of magnums and carbines but the same three laser / plasma weapons
No stealth options
Governing stat of Perception isn't as valuable as having a high Agility depending on your character build
Previously Energy Weapons held onto crit builds as their time to shine. Most featured low base damage with a generous critical chance and high critical multiplier. Unfortunately most Guns now boast the same.
Laser is highly accurate and a high rate of fire but has low damage. Plasma hits like a neon green battering ram but is slow moving so you can find yourself missing outside of V.A.T.S a lot if you don't compensate. Generally I find most people who dabble in Energy Weapons prefer to go one route or the other, I'm a Lasers man myself. With the mods that come with the basic game and GRA I can make a lot happen with the Pistol, RCW, Rifle, and Tri-Beam.
Energy Weapons boasts some ridiculously high damage heavy hitters that are a royal pain to maintain in the form of Gauss Rifles and the Holorifle as well, these compete (on paper) with the heaviest hitting rifle but the cost of maintenance is a bit tedious.
Guns Pros :Almost everyone is using one. Even if yours breaks you'll find something to repair it with or pick a new one off of Corpse-Mart
EVERYONE except the Van Graffs sells Guns ammunition
Numerous concealment options for Holdout weapons
Numerous silencer and scope attachments to let you switch between fully automatic machine gunner to stealth assassin with ease
Guns specific perks such as Grunt and Cowboy do a hell of a lot more for a hell of a lot more weapons than Laser Commander and Plasma Spaz do.
Guns Cons :A lot of the big boys have hefty strength requirements, but this can be meted out with the Weapon Handling perk
Reload times depending on the weapon you're using, especially true for most revolvers and some clip / box fed chuggers.
Have to use specialty ammunition depending on the type of enemy you're fighting - meted out by Hand Loader for some weapons and the fact that Hollow Points overpower high DT depending on the gun you're firing them out of, RE: Brush Gun
I probably missed some, but there ya go.
They're comparable in the early game and mid game. Late game I have to say as much as I love Lasers, I've never had it quite so easy as using a Brush Gun or an Anti-Materiel Rifle.