Why does this movie get flak for the CGI?

The "dreadful CGI" still seems to be quite a popular argument among Deep Blue Sea detractors, both on this board and elsewhere. But really, the computer-generated sharks don't look THAT bad for the most part.

Yes, the VFX have definitely aged, but that's to be expected giving the time this movie was made, its budget, and overall genre.
In fact, I'd say CGI of this quality was very much a standard for action films that came out during the mid-late 90's - The Mummy (1999), Godzilla (1998), Jumanji, Armageddon, and other action/disaster popcorn flicks of this time were all effects heavy and weren't any better or worse than Deep Blue Sea in terms of the CG use.
And while you could argue that Jurassic Park, Titanic (1997), and The Matrix were all from the 90's and yet had better effects, those movies were very impressive feats for their time and many other filmmakers and VFX artists were struggling to catch up.
Not to mention, I've seen far worse examples of CGI use in films made well into the 2000's and even the 2010's - The Flintstones in Viva Rock Vegas, Hulk (2003), X-Men Origins: Wolverine, Star Wars prequels, and Green Lantern are just a few examples. And it doesn't help that a lot of these movies were made on larger budgets!

But even if the CGI doesn't hold up well in Deep Blue Sea, the film still makes excellent use of animatronic model sharks which have stood the test of time. The design, texture, and movements are all incredible. There's no denying that!