First, you might want to delete the third sentence of your post. It puts you squarely in violation of SubSim's policy on software piracy: "
We do NOT allow discussion or even mention of game piracy, warez, peer-to-peer game swapping, game cracks, illegal download sites, or illegal file-sharing." They do enforce this.
Second, if you take a look around this forum, you will find that many people play GWX3.0. From their posts, you will see that GWX performs well and is pretty much bug-free. GWX3.0 has an excellent reputation for stability. From my own experience and that of many, many others, I can assure you that the problem you have experienced is not inherent in GWX.
But you have had a problem, and that problem is a fairly common one. Again, take a look around this forum and you will find that CTDs when loading a saved game are a common complaint. Occasionally this problem can be caused by a faulty mod. But usually it is due to actions by the user and is preventable. The GWX manual has a discussion of some of these causes, beginning on page 13. It's definitely recommended reading. Note that all the causes discussed there are inherent to SH3 itself, and
will be experienced with any mod you care to install.
Some of the problems are due to poor software hygiene. Activating or deactivating any mods while on patrol can cause instability which will show up (not necessarily immediately) as CTDs on reload of a save. Saving over the top of a previous save (using the same name for a save without first deleting the old save) will cause CTDs on reload.
But all of these things are independent of the mods you have active. In fact, the issue of saved games failing to reload is endemic to the entire SH3,4,5 series, and is just as likely to afflict you when playing rockstock SH3. But if you follow "a few simple rules"

, you can count on reliability and enjoy the game. DO read and heed the discussion of "
Known Silent Hunter III Issues and Workarounds" in the GWX3.0 manual, all 5 pages (!) of it. It will save you grief whether you play GWX, rockstock, or any other supermod.
Now to answer the question you posed: GWX3.0 is preferred by a majority of SH3 players, but two other popular supermods are LSH3, and my favorite, NYGM. NYGM is generally agreed to be the most historically accurate in terms of gameplay and results. "NYGM doesn't have the best graphics, but it gives you a nice, accurate death." LSH3 and GWX both have more eyecandy and curb appeal, and the difference between these two is a matter of personal taste, although GWX is by far the most popular. It also has the largest number of compatible add-on mods made for it, so you can pretty much make it exactly what you want.
Since you already have a clean install, you are ready to load whatever supermod you choose. But don't reject GWX because you believe it caused your CTDs. It didn't.
Good luck and good hunting.
And do get rid of that third sentence before the "cops" come to call!