I love my Pike. It was the first ship I mastered, and when I'm in a close match where I feel like I really need to maximize my contribution, that's what I fly. First, it can be extremely survivable -- when you need to go defensive, power to shields and ducking and weaving around the environment makes you very, very hard to kill. Add a little situational awareness and you can keep a satellite from being capped for a good long bit, unless you get ganged hard. When I'm going up against the better pilots on my server, it gives me enough survivability to be able to get out of a lot of sticky situations. Barrel roll is a lifesaver too, and it's also good for quickly jumping on nodes as soon as a domination match starts. Basically, anyone can kill enemies if they're left to just go shoot them unmolested. With the pike, I find I have more time to react when I get jumped so that I can try to either escape or turn the tables before I can get taken down. Quick-charge shields and hydrospanner can be lifesavers too.
Offensively, I go with quads and primarily concussions. I started with protons, maxed those out, and have switched to EMP missiles. The only problem with those is that I forget that I have them since it's not a habit yet, but they seem useful against drones/mines as well as enemy ships. Maxed quads with power to weapons is a force, and in a head-to-head with scouts, I can start locking missiles a little earlier due to the longer range. They lock faster, but once I launch, I can barrel roll right at them, evading theirs while mine hit. As I go head to head, I use the quick-charge shield after I've taken some damage to fill them up and pop hydrospanner too if much gets through to my hull.
I find there's no ship type that I have trouble with in my pike -- just good pilots. It's got the speed and closing ability (especially when you use barrel roll OFFENSIVELY) to deal with gunships, is nimble enough to deal with scouts (though in the hands of a skilled pilot, can be hard to get a bead on), and can pound away at bombers and their drones/mines. I've mastered at least one of each type, and while they all have strengths and weaknesses, for my style, I just like the pike best. I'm sure there are some who feel the same way about pretty much every other ship too. But I wouldn't say it has any major flaws, and it very well might not be you either -- it could just be that your natural style is more suited to another ship.