I've been an avid weightlifter/bodybuilder for the past 15 years, and only found cycling this past year as a solution to my quest for cardio without boredom.
Regarding squats, it is better to do a full squat with less weight than a partial squat with greater weight, unless you want lopsided development of your physique and strength. Squatting lower than parallel is not necessary, and those extra few degrees put tremendous tension on the quads' insertion tendon (which is stretched over the knee joint) with little benefit. It's just not necessary, and I've witnessed one person tearing the tendons in both knees from this(!).
What I recommend is the following:
Pre-exhaust your quads and glutes on a plate-loaded, seated leg press. I perform 5 sets of around 12 reps each, using increasing weight (stepping from 450lb up to 900lb) and good form. The leg press does a good job of pre-exhausting the strongest part of the quad.
Next, go to the Smith rack and perform your squats. I perform 3 supersets of 12X12 reps (back to back) alternating wide stance and close stance, using only moderate weight (increasing from 135-225lb) and performing the full movement. Since you're already pre-exhausted, you don't have to test your back using heavy weight. You will find that with your strongest part of the movement (toward the top) pre-exhausted, your strength through the movement will be fairly even. It will be difficult to walk immediately afterward if you do it properly.
Finally, finish with three sets of leg extensions, using moderate (but increasing) weight and good form/concentration.
This type of regimen works well because it will evenly distribute your quad/glute power, and is very easy on the knees and back. I always get inquiries/complements about my leg strength and physique, so I can attest that after years of experimentation, this really works, and best of all, it is SAFE.