I'd personally go with the MR3's. I switched over three seasons ago, and love the results. Here's my breakdowns of the pros and cons of both the MR2 and MR3 (cut from a previous post).
I really like the MR3 and have switched all my guide reels over to this model. The MR3 is lighter and has a larger arbor for quicker line retrieval. The later, is really important when inexperienced guests are playing a fish that is running back at the boat (especially big springs). Furthermore, because of the larger arbor, knobs are spaced on a wider diameter which I find is a more natural turning radius (try retrieving a 100 feet of line on a fully spooled MR2 then on an MR3, you'll find your hand muscles are less burned after doing so on the MR3).
I find line retrieval speed really important when playing fish, and I keep my reels fully spooled for this reason. To cut down on line costs, I spool my reels with more dacron backing than most (~3/5 of the reel capacity). When the mono level gets low, I simply remove it while keeping the backing. With the larger arbor of the MR3, I re-spool less often, and waste less monofilament.
I really appreciate the interchangeable option of the MR3. I retrieve left handed, while most guests are right handed. The MR3 allows me to have a useable personal reel at the end of the season. Also, left handed guests appreciate being able to use a high-end reel (In my experience, most saltwater guides do not carry high-end left handed mooching reels). If you are converting from left-handed to right-handed or vice versa, the process takes about 15 minutes using a line spooler. You need to de-spool the reel entirely, open the reel and reverse two clickers, close the reel, and then re-spool.
To gain the interchangeable spool on the MR3, the free spool had to be removed. Some people see this as a huge disadvantage to the MR3. Personally, I don't mind, I usually fish with weighted rods, and typically in the top 50 feet. If I need to drop to bottom, I can reduce the drag (it takes about 10 seconds longer to hit bottom 200 feet down with an 8 ounce weight on an MR3 drag removed, versus an MR2 using free-spool).
The MR3 has a larger cork drag system with a buttery smooth adjustment knob. When the MR3 is well oiled and greased, I prefer its operation to the MR2. It sounds better (in my opinion) and applies drag pressure more consistently which can also be more finely tuned during the course of the fight. On the down side, I find I spend more time maintaining my MR3's than my MR2's. During the season, I re-grease/oil my MR3's with perforated back every 70 hours, my MR3's with solid back every 100 hours, and my MR2's every 140 hours (I cut these numbers in half when it rains regularly).
The drag knob on the MR3 is larger and easier to make fine adjustments. On the downside, when inexperienced guests are playing fish, you need to be careful that they don't accidently rub their knuckles against the drag knob while reeling (especially when wearing gloves). This results in accidentally tightening the drag and can end in loosing the fish (I've seen guests do it frequently, but warn them when I catch them, and can only attribute loosing two fish to this cause in the last three years).
On the whole, both are great reels, I just prefer the MR3.
