1. The GGnM has a lot more to master than those fruits
2. What flaws?
Oh no, it really doesn't, there's a much higher level of complexity to mastering a Logia than there is to mastering a Paramecia or Zoan as you have to deal with elemental weaknesses, transformations, creation and manipulation all within one fruit. Whereas Paramecias in most cases have a very limited scope of power. Luffy is very creative but he is by no means a master
Flaws?
1. He can't stand up
2. He can't stop bouncing around (hence the name "Bounceman")
3. It'll likely be incredibly painful/fatigueing during or after use
1. Doflamingo: Strings have been manipulated to the most versatile possibilities with Doflamingo, as an enclosure, to control and manipulate, to fly, to heal, to cut, to sew, to defend, everything. And there are no weaknesses to the fruit because of his incredibly skilful usage
2. Shiki: Shiki managed to turn the ability to make things float into manipulating the shapes of mountains into f*cking lions and throwing them at opponents, nuff said really.
3. Crocodile: He's been the most successful character at eliminating his weakness by developing the technique to absorb moisture and in turn defeat his own weakness, he's a skilled transformer (as shown by being able to avoid Seastone nets), and has mastered a huge depth and bredth of techniques
4. Enel: Same as Crocodile
5. Law: This Mofo can warp himself, objects, operate freely, edit the world around him etc.
That's a lot more than Luffy can do. All he does is stretch and use gears which are detrimental to his health