Come again?

In otherwords dont waste money on something that you have to mod to make it work right

That depends on how you look at it.
If you want something that works properly straight out of the box then you would be right.
If you are willing to do some work yourself (and spend a bit more ) then the Cougar would just be a 'component' of your new HOTAS, the other component being new gimbals.

To answer the question of what is the best HOTAS you can buy, one's criteria should be defined first whether it be cost, durability, programmability, flexibility, number of physical button presses, number of hat switches, number of rotary switches, design, ergonomics, etc. or any combination of the above.

A modded Thrustmaster Cougar utilizing NXT and Hall sensors isn't the best if one's criteria is the total number of physical button presses, the HOTAS with the most number of hat switches and being able to bind a CH Fighterstick, CH Pro Throttle, CH Throttle Quadrant and CH Pro Pedals (or even the one of the CH flight yokes for bomber/civ virtual pilots) as a single device in the joystick control panel applet along with a more clear visual aid in what mode selection you are in.

I'm just citing this as an example as all the setups have their strengths and weaknesses. My ideal HOTAS would be the comfort and rubber textured grip of the Saitek HOTAS, the number of physical button presses and hat switches and quality engineering of the CH Products line and the metal construction and fidelity of a fully modded Thrustmaster Cougar.

If you define the criteria, then what is the best HOTAS for you can easily be determined.

CH fan here all the way. I had a Saitek X36 and a Saitek X45, but never had a real HOTAS. So a couple years ago, with the encouragement of a friend who shall rename nameless, I bought a Fighterstick, Pro Throttle, and Pro Pedals. Never regretted it for one instant and I'm still pleased as can be with it and the Control Manager.

Kudos to CH Products and Bob Church.

I also have had the TM Cougar, Saitek X45, X52, X52 Pro. Now I own CH products. They are simply the best bang for the buck.

Right now, I'm using a Thrustmaster HOTAS Cougar that came pre-modded with the original Force-Controlled Cougar, and some RCS pedals with a Hall sensor kit installed. It's pretty reliable thus far, though the Y axis of the microstick has a strange response when pushed up. (Of course, since the stick is modded already, I've never had to deal with the pot/gimbal problems many stock Cougar users encounter at some point.)

I used to own a CH Products Fighterstick and Pro Pedals, both USB. Very fine products, and the Control Manager is still unmatched for programmability-and yet I sold them when I was short on funds. Why? It all boils down to ergonomics-the Fighterstick handle just doesn't feel quite right, and the Pro Pedals are too closely spaced for my liking. Ergonomics are very important if I'm going to be having my hands and feet on these things for long periods of time. The other factor was that I specifically bought this particular Cougar for use with Falcon 4.0, as it's the most faithful of the consumer HOTAS setups to the F-16's controls. (The Fighterstick only has a single-stage trigger and no paddle switch, and the Pro Throttle doesn't even remotely resemble the F-16 throttle!)

Of course, there's a new player in the market that very few of us can really comment on at the moment, that being the Logitech G940. I'm hoping to get one to complement (NOT replace) my Cougar, as the deflecting FFB stick will lend itself better to prop jobs (the FCC mod in my Cougar makes it very stiff with little deflection) while the split throttle is better-suited for dual-engine aircraft. I'll switch between sticks and throttles depending on what feels right for the aircraft I'm piloting at the moment, basically.

Ya forgot about the money bit

My choice of stick is currently a stock Cougar too, and it was my first proper HOTAS too, purchased on the grounds that I won't be able to break a stick at the base if it's made of metal. Like many of the other guys here, I've probably gone through the same issues; misaligned speedbrake/dogfight switches on the throttle (I don't know what it's like with the later batches) and the usual pot problems, and the existing stock gimbal system has a much larger throw than I'd prefer.

I think that if you want something that works out of the box, go CH. If you want a system that you can turn into something very professional, then Cougar + mods, but obviously this has a high overhead.

Going on a tangent slightly, how does Foxy compare to the other stick programming software kits that you get with Saitek and CH?

I like my CH setup. It may be plastic, but it's durable. It worked great right out of the box. Very accurate.

Owned an X45 in the past and stopped working correctly pretty quickly. I had read that a lot of people had issues like that with the X45, and with some more of the same with the x52 models, so I decided against purchasing Saitek stuff again.

Cougar, while it looks neat, is just too much work. I didn't like the idea of being required to spend a lot of money modding a joystick just to get it to work properly.

Yep, Cougar with FSSB R2 here, new dogfight and speedbrake switch sliders and hall effect mod in the throttle...