I have used all three of these ships to a great degree in trying to determine which ship I want to settle down in as my 'main'. Each one handles differently and has its perks and cons. In the end, it comes down to personal preference on your fly style, but here is my two cents.
Wall of text incoming!
Clipper- Absolutely love this ship. Out of all three, it is certainly my favorite to fly. There is no matching it's speed and those who say it has poor manuv haven't flown it properly. I can run circles on my own smoke trail - I can turn around so quickly. It may have the worst Vertical thrusters for general up and down movement, but it has the highest ptch and yaw speed of all the larger ships. It takes a certain degree of practice to use it effectively, but if you learn, you can run circles around Vipers (I know, I've done it

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Pros - It is fast. Faster than any ship in the game except for a fully stripped down Cobra. It has 400 tons of mass to use as a great weapon. Anything you can't hit with your guns, you can decimate with a speed ram and watch them bounce off your shields. I knocked a Cobra down to 27% in one ram. It has enough internals, more then you can probably make use of. It has the power management of a god.
Cons - It's shields are pretty low. Improper outfitting can easily leave you in trouble if you try to take it into combat. It can be expensive to outfit fully. In rough costs (not including armor), it can be about 80 mil fully outfitted (Also not including the A7 shield generator, which is 51 mil on its own). Huge landing pad open. Closes doors to outposts.
Python - I picked this up immediately after having flown the Clipper, and can honestly say I was a bit disappointed. Both of these ships have superior internal compartments and power management. The python is slow though. Painfully slow. Coming from a clipper, that speed loss can really be felt. But man does it run like a tank. Arguably the hardpoints on the Clipper aren't the best. They are superb if you run gimbaled, but that can lead to chaff problems. The Python doesn't have this issue at all. Its hardpoints make it seem like it was designed as a weapons platform. If you can get it in your line of sights, its decimated. But no joke, that's if you can get it in your sights. Its manuv is worse than the Clipper in certain aspects. It has superb general thruster movement, such as vertical thrusters. But its general yaw and pitch abilities are terrible. It takes some practice to get used to, and even more to use it effectively. May want to consider some flight assist off lessons for this ship if you haven't learned that already.
Pros - Shields are great. The main difference between the Clipper and the Python is Shield/Speed. That's why I say it comes down to personal choice. Determining which one you fight better with goes a long way. Power mangement is god like. Combat outfitting still leaves room for ample cargo capacity, and this ship can trade with the big boys. It can hold its own in a fight, but don't expect to run from equally large vessels. Unlike the Clipper, if you can't win.. you can't win. That extra hardpoint can come in handy, but it is only one more hardpoint. If you can't land your shots, in my opinion it isn't worth it. Clipper is outgunned, but only by a little. Python is a beast though. Even post-nerf, it runs like a hardcore heavy tank with tank buster equipment. Jump range is about the same for these ships if fully combat outfitted. You may be able to get more out of either if you sacrifice a few things. Medium landing pad.
Cons - Slow as can be in most regards. Like I said, takes some practice to learn to use this ship effectively against smaller vessels. Expensive as hell to fully upgrade. A-fitting with no armor can easily surpass 100mil. Probably closer to 140 mil for full A grade, not including armor.
FDL - This ship has some pros and cons that make it interesting to fly. I find that it is an odd cross between several different ships in this game. Power management is certainly similar to the vulture. This ship is like the odd cross between a vulture for the power/heat, a clipper for speed, and a python for shield strength. That being said, the shields on this thing are insane. You can outfit it with the class A4 shields and keep that A5 for cargo if you want. In which case you have a 32 sized cargo bay. Good enough for smuggling and odd cargo jobs. The A5 shields are pretty much overkill in my opinion, especially for PVE. I don't hesitate to take this ship into a SSS by myself with even the A4. Im comfortable against 3 of the newer NPC Annies in it. Then again, I felt that way with the Python too, just a bit more reserved due to turn speed against the smaller ships that are often there. Turn speed on the FDL in general is better than the Python. I would say the Python has better Vertical and lateral thrust capabilities, but the FDL has better yaw and pitch abilities. It has a hard time against some of the smaller vessels, but not nearly as much as the Python. If you can manage the Python, you can certainly manage the FDL. The weapon placement is tricky. You can easily get all 4 of the upper hardpoints firing on target, but not so much all 5. That huge hardpoint can be troublesome. If you outfit it with certain weapons, you can certainly see a crossover arc where the upper and lower can't fire at the same time. To be expected I'd suppose. In terms of killing ability, it is on equally footing with the Python on smaller vessels. The class 2s are plenty powerful for that job. It can have some trouble getting past the shields of larger targets though. But once you're through, the hull drops like you hit it with a bomb. Especially if you are using that class 4 cannon or PA. This ship can be ran with outfitting even tankier than the Python. It can be EXTREMELY troublesome to kill if the pilot knows what he's doing. Likewise it has speed on its side. If it can't win the fight, it has a max boost speed of 400, so it can certainly get away.
Pros - Immensely powerful shields. Workable weapons. Plenty of utility slots (6 of them) for different items. You can actually run those shield boosters and still have extra slots for other stuff. Cheap to outfit. You can outfit this thing A grade for little more than 70 mil, not including armor. Medium Landing Pad like the Python opens doors to outposts.
Cons - Certainly not a multipurpose. The A5 can take you places, but doesn't compare to the other two in regard to internals. Overheating can be hellish in this if you try to run all beams. Jumprange is pathetic in comparison to the other two, but decent in comparison with the vulture. Vulture can still get higher in full combat loadout though, so keep that in mind.
In the end it all comes down to preference and which ship you enjoy flying more. If you are looking for something that will be the next step up from the Vulture in combat, you can stop there. The Vulture is the perfect balance between cost and income per killing ability. It can kill to the maximum extent of spawn rates for RES and CZ without the need to bug out after extended combat. Once you reach the Vulture, the other ships are just overkill. Sure they can kill faster, but they also cost more to run, cost more if you die, and are limited by NPC respawn times. In terms of PURE COMBAT, I would run the Vulture or even the FDL if you really want. I found those two the most effective for solely combat ability. In terms of multipurpose roles, Clipper and Python are pretty well matched in my opinion. It just depends on your preferences. Combat for PVP with these 3 is completely different than PVE. I have found that all of these ships are effective in PVP if placed in the hands of a pilot that understands their ship to the full extent. Even the Clipper.