My two biggest complaints about it are too little deadlift volume (and always deadlifting after you've squatted, which is just suicidal at higher working weights), and no periodization. The latter is really the biggest issue with it as anything beyond an introductory program - the benefits of periodization are well-established, and while linear progression is great as an "on ramp", the human body just can't sustain that style of progression indefinitely. When you hit the point that you stop regularly progressing linearly, it's time to stop and switch to a periodized program.

If you wanted to get really picky, it lacks lacks arm (bicep and rear deltoid, primarily) and oblique accessory work, but I don't really consider those too big of a problem since most beginners need something straightforward that isn't too overwhelming.

Any suggestions for a periodized program?

5/3/1 is my personal choice.