If, for example, a protoss opens with a very aggressive opener then falls back to expand:
(advantage) He has more units early on
(disadvantage) He has later macro/tech
^This is the kind of stuff that makes Starcraft exciting. It's the fact that when you do one thing, or open one different way, you get something and you lose something.
If you make a 10 cannons at every base to defend mutalisk harass:
(advantage) You're far more secure against mutas
(disadvantage) You're way behind on minerals because of the investment
Smart players eventually find balance between situations where you get one thing or the other. For example, the old TvZ opener (before queen buff) where the Terran expands and harasses with 4 hellions- the terran gets to grab a quick expansion while putting on early pressure. Great! This is what makes one opener better than the other.
But this is not the case with warp gates. To reiterate, there's no advantage to using gateways over warpgates. It's like having marines and supermarines that come from a barracks, and they both cost the same except that the supermarines do 2x the damage.
If I was to 3gate expand with no warpgates:
(disadvantage) My units come out slower
(disadvantage) My units cant come out anywhere where there is power.
Do you see the problem? Warp gates are meant to be special because "ooh you can warp in anywhere" but there HAS to be some kind of disadvantage to it. Almost anything you do in starcraft has an advantage and a disadvantage, even if they are minor, but warp gates lack this function, thus making the gateway absolutely useless, and thus just being a double disadvantage.
Another problem with warp gates is that the whole concept of defender's advantage is completely nullified. Both zerg and terran have "home advantage" in many scenarios. For example, the guy in the zerg's base can be surprised by a huge batch of lings and take out the attack, or terran has bunkers at home which he can repair. These are advantages that these races most likely wouldn't have on the opponent's front doorstep. Now protoss, has nearly the exact same advantages as if they were to warp in at the enemy's doorstep or at their own doorstep. So many games, especially RTS's, have this concept of "defender's advantage" (heck, even Tug of Wars have a defender's advantage when you think about it). Warpgates nullify this, and gateways have the potential to fix this!
My suggestion to fix? Consider lowering the build time of gateway units or raising warp gate units' cooldowns to the point that protoss players feel that there exists a reason to switch back to a gateway rather than a warp gate. I know that this would be a pain in the butt to balance, but give it a try:
(advantage) My units build faster!
(disadvantage) My units only come out through the gateway.