It's never too early to make these comparisons.
Anthopoulos' regime was very flashy in how they collected prospects. They aggressively collected compensation picks under the old CBA, and under the new CBA they made a habit of drafting players that would be tough to sign. They used a bit of a gimmick where they would draft a handful of way under-slot seniors in rounds 5-10 in order to theoretically fund the signing of one or two risky picks each draft class. It should be noted that some of these senior signings actually worked out, such as Kendall Graveman ($5000 bonus). But the vast majority were essentially punted picks.
Anthopoulos' regime was inclined to take high school players, envisioning this as the player pool with the highest upside. They were also inclined to taking pitchers. As a scout-first front office, the inclination towards pitching was largely based on the notion that it's just easier to scout pitching. Of course, it's common sense that high school pitching is the riskiest draft commodity there is. In spite of this it seemed to work for the organization; from 2010 to 2012 the draft produced for Toronto players like Sanchez, Syndergaard, Norris, and Stroman, along with some nice late-round surprises like Pompey and Pillar. But the organization could not hit on a single highly-selected position player, except for Alford in 2012. That trend continued for 2013-2015, and the well-spring of nice pitching seemed to dry up too. 2013 and 2015 look like particularly lean draft years. A consistent failure to sign high draftees plagued the Blue Jays. They made it their MO to take tough-signs, but deferring development on a high draft pick every single year starts to hurt your system after some time. It's fair to question a lot of the Anthopoulos regime's draft strategies at this point.
Expect Shatkins to run a much different draft process, every year. This is a front office that actually uses and appreciates statistical information and evidence. You won't see them draft a bucket of high school pitchers in most years. Expect a relatively balanced draft that leans college and leans position side, but without any strong biases or gimmicks. They might take 2/3 college players with their day 1 and 2 picks, but they'll definitely take a high upside high schooler if it's the best player on the board.