My school does all the basic sciences in one year and you go straight to your core clerkships in second year. We take Step 1 during 3rd year (dedicated to research) and it works out great.
You will notice on step 1 that the vast majority of questions are essentially a clinical scenario followed by a basic science aspect of the problem. Recognizing the clinical scenario is the first and most important step to answering the questions. Having a year of clerkships under my belt made recognizing the scenarios inifintely easier. I dont care how many times you read about pulmonary emboli in basic sciences, the bottom line is, the presentations of PE given in a Step 1 question is classic and mimics the real life scenarios you see and work up during clinical clerkships. It's a million times easier to remember clinical scenarios when you've actually seen them and not just read about it.
Also, for us, when it comes time to take Step 1, you have already seen the basic science at least three times...
1. When you learned it first year
2. When you reviewed and relearned it during clerkships
3. When you officially sat down to study for Step 1
Essentially, Step 1 and 2 CK have the same question stems (clinical scenarios). The difference is that the question is more clinical in Step 2. For example, they will present a pt with an infection. On Step 1, they ask for how the organism will stain. On step 2, they would ask you what antibiotic works best.
With this said, it's absolutely no coincidence that people generally find step 2 inifintely easier than step1. It's because the clinical question stems stay the same and you have seen them on the wards. It all comes down to recognizing the clinical scenario first.