Suggestion please: How to improve sound.

As a new comer to audio world, I gradually build my system:

Theta Data II transport.
Theta Pro Basic II DAC.
Audio Research LS-15 tube preamp (superb).
Aragon 8008 Mk2.
NHT 3.3.

All cables are Monster's at this time. For speaker cables, DIY cat5 is on the way. I am using gauge 12 generic cable now.

This system sound pretty good to me. However, I feel it should sound better. The only A/B test I did is to compare preamp to Myryad MP100 and Threshold F10, LS-15 sounds absolutely better, smooth and more musical. I also compare Aragon amp to Threshold S300 and seems NHT 3.3 likes power.

Overall, I feel this system could sound more transparent and more airy. Since I have no chance to do many A/B test to pickup the best equipement, I would like to hear some comments from real audiophiles here. Which is bottle neck in my system?

But I don't have too much money to burn. I once heard Pass Lab X350 which superb, but it is just too expensive. I was thinking about Aragon Palladium. I wonder if upgrade from 8008 to Palladium with more power will improve a lot?

Any comments are welcome and thanks in advance.

Spend a lot of time working on set up and treatment of your room (even if you think you have done this - revisit it). You might be amazed at the differences small changes can make - often much greater than buying new stuff. For example, in my room, which I thought was well dialed in, I moved one speaker closer 1 1/2 inches and the other 2' further to toward the outside (no longer symetrical) and the sound stage clicked in like I couldn't believe! The first time I have ever had great layered depth of imaging in my present room.

Re new stuff, what kind of sound are you looking for - what about your present set up do you not like? Give us a clue and I'm sure you'll get some meaningful recommendations.
First you need to assure you are getting the most from what you have. You will need to account for speaker placement and listening position. The size and shape of your room will affect where your speakers will sound best and the ideal listening position. Take some time and experiment. Move the speakers around and adjust the angle of the speakers. You'd be surprised how much of a difference this can make.
The NHT 3.3s are real good speakers, but they are demanding about setup. Make sure that they are absolutely parallel to each other and be prepared to spend alot of time experimenting with the distance from the rear wall. They like power, but changing amps won't make that much of a difference. The downside of the 3.3s is that they don't do the transparent and airy thing as well as some other speakers. Their strong points are dynamics, imaging, bass and overall smoothnes and you'd be hard pressed to find a speaker at its price that betters it in this combination. The lack of transparency and air is a relative thing, not a fatal flaw.
For a minimal investment you can buy Robert Harleys book "The Complete Guide to Highend Audio." It offers a number or set up and placement tips which can be done for free. Laura Dearborn's book "Good Sound" might be helpful too.

Generally speaking it is cheaper to treat a room that it is to buy new gear. It can also be much more satisfying.

Good luck.
Treat the rear wall behind your sytem and maybe a couple feet out on the ceiling and walls. This is the LEDE(live end dead end) practice and works excellently. Room treatment is extremely important and will affect the sound ALOT. Electronics and cables are usually pretty small changes, room treatment is major.
All the above posts are correct and will help. Don’t forget after the above are tweaked that dedicated AC power outlets on their own circuits and clean AC power is also going to make an improvement (after the above suggestions are taken).
I like what's mentioned above. I've sold the 3.3's for years, and am familiar with sound.
What you might want to sometime consider is a differnt amp with those, and even "bi-amping"! If you found an amp who's midrange and trebble where pristing sounding to your ears on those speakers, you could easily pick up something like a Parasond HCA1500, 2200, or 3500 to drive the bass woofer(bottome posts), and a sonically superior Pass X150 or something on top!..which would go good with those speakers probably.
Bi-amping these speaekers would give you more dynamics, and a better "top end" option optimally. Heck, you could even try tubes up top if wanted. Otherwise, there are much better amps out there than the 8008(I've sold and owned that amp). And bi-amping would give you the power and flexibility. Also, try upgrading tubes on the LS16, which I've also owned/sold over the years.
Acoustics, set up, source matching, cabling, power conditioning, and tweaking is the other steps. good luck
I might be repeating what has already been mentioned by other members but what you can do to optimize your system is
(1) work on treating your room. There is some excellent info on the WWW. Use your favourite search engine & type "Jon Risch". You'll learn about tube traps, high freq absorption using panels & lots more stuff.
(2) Work on speaker placement. You can get info from Cardas's website & from the Audio Physik website.
(3) If you have not already, spike your speakers. I suspect that the NHT 3.3 are already spiked by design (?).
(4) Work on isolating your CDP & DAC from your rack. Various methods are available for this depending on your budget. Using ceramic or carbon-fibre cones is a start. You can also build a Symposium-like DIY platform. You can also use an inflated bicycle inner tube for isolation. Some other audiophiles have created a hammock-like suspension system & their CDP & DAC is slung from this suspension. Search the Audiogon archives for more info. In the isolation dept. the sky's the limit in terms of ideas to isolate gear from the rack.

If you pay attention to the room itself, the gains from that are plenty to take your system to another level. It is, sadly, the most forgotten element in most people's 2-ch setup!!
My experience is somewhat dated, but I believe it may be as relative today as it was when I was heavily into getting the most out of my system that I could for the least dollar input. Spikes everywhere may be the most cost effective, and the amp-preamp interconnect is extremely important. Finally going to MIT from Mark Levinson silver, and a variety of copper interconnects provided the most musical and spatial result I found (Note: PV5 pre & Quicksilver mono amps). Good luck.