My opinion is that Daniel Murphy should be starting at second base for the Mets for the short-term future (two to three years) at least. I'll do a multi-faceted comparison to back my opinion.
Daniel Murphy has average range and rates as an average overall defender at second base this year and last. He will make the occasional error, but he will also make the occasional crazy-good play. That evens out to average. Also, I cannot stress enough the value of a proven product. The Mets know what they have in Murphy's defense and it grades out as passable.
Scouts contend that Wilmer Flores' most valuable position on the field right now is third base. He has grown to 6'3" and he does not have the agility to man the shortstop position. From what we've seen in limited reps at third base, Flores seems to be a capable and sometimes above average third baseman. Unfortunately, we're not evaluation Flores as a third baseman. His lack of first-step quickness and agility lead scouts to believe that Flores may have trouble manning second base. I know he's been injured as of late, but Wilmer doesn't quite seem flight of foot either. I think playing comparable defense to Daniel Murphy is Wilmer Flores' ceiling, with playing a Dan Uggla-esque shortstop is probably where Flores grades out.
Daniel Murphy: 75 / Wilmer Flores: 55
2. Hitting for Average
Daniel Murphy has shown that he is a capable hitter at the plate. Although he is currently batting a BABIP deflated .277 (BABIP is .305 this year compared to .329 last year), Murphy has shown that he can hit a consistent .290 over the course of an entire season. Murphy is also currently in the top ten in runs scored this year, even with a lower batting average this year. Although he goes through his hot and cold streaks, his batting average and on base abilities usually level out to .290/.330. Murph consistently has a 40 OBS+ (a stat I like to use in evaluating propensity to walk or reach base independent of hitting prowess (OBP-BAA)) which grades out about average because he does not walk frequently. He also is capable of scoring 80-110 runs for in a more potent lineup. His walk percentage and strikeout percentage are 4.4%/13.5% and are both acceptable rates.
Wilmer Flores has hit well in his minor league career. He has hit .260 in the majors thus far and that's probably a good estimate of how he'll hit in the future. No scouts think he'll hit .300, but I can see .285 being his ceiling. Wilmer Flores has provided a very similar 40 OBS+ in his minor league career and in his first Major league games. His walk and strikeout percentage are slightly better than Murph's at 6.0%/12.0% and they are believable rates given his minor league work.
Daniel Murphy: 85 / Wilmer Flores: 75
3. Hitting for Power
Daniel Murphy's career single season high for home runs is 12 and he's on pace to do about the same this year. This is certainly not the most valuable part of Murph as a player but he provides serviceable value with the occasional home run. However, Daniel Murphy had 49 XBHs last year (40 doubles) and is on pace for 49 XBHs again based on ZiPS projections with about 36 doubles. Overall, Murphy is slightly below average in this department as he'll only slug slightly above .400 with a .121 ISO.
Power is perhaps Wilmer Flores' best tool and biggest asset. He boasted a somewhat Vegas-inflated .531 slugging percentage at AAA last year and has really grown into his power as he has become bigger in size. Scouts project that Wilmer will be at least a 20 HR threat with about 25 or 30 not totally out of the question. He is a run producer. Wilmer definitely wins this category.
Daniel Murphy: 70 / Wilmer Flores: 90
Daniel Murphy has shown some impressive agility this year on the bases. He's on track for 20 stolen bases this year and his roughly 80% success rate is above average. His Baserunning runs above average is 4.2 and his FanGraphs speed is 5.9, both rating in the top 25 players in baseball. Ipso facto, he takes the extra base and he steals bases well. Murph has added another dimension to his game this year and it's certainly encouraging.
Wilmer Flores has not stolen more than three bases at any level of professional play. He had a FanGraphs speed of 3.9 in AAA (I can't use his speed from the Majors because the ankle certainly isn't helping him run faster) and that rates just below average based on the fact that the speed has a 4 component value. There is one active player with a 3.9 FanGraphs speed value: Wilin Rosario, the Rockies starting catcher.
Daniel Murphy: 90 / Wilmer Flores: 65
Daniel Murphy has become the second-in-command in the Mets clubhouse in recent years. He's a leader by example based on his hard work and flexibility when it comes to the Mets ever-varying plans for him. No better example can be found than when he got himself tossed yesterday in the 10th after continuing to argue a bad call after Chris Johnson had hit the go-ahead homer to put the Braves on top. Murph was defending his teammates by getting himself run and that kind of fire is something that the Mets had present on the 2006 team (Paul LoDuca) and the 1986 team (Lenny Dykstra and Wally Backman).
Wilmer Flores is a third baseman right now plain and simple. Putting him at second base diminishes his value for the Mets. Trading him as a third baseman may be the way the Mets get the most value out of him. Nevertheless, Wilmer has played with poise at every level of the minors, being in the top 5 youngest players at each level and that counts for something.
In the end, Murphy and Flores grade out like this.
Daniel Murphy: 320 / Wilmer Flores: 285
Some of this post has been conjecture, and I fully agree that there is some latitude in some of my evaluation. Flores could grade out similarly to Murphy with some progression or regression from the two. But it's plain to me that the Mets have a good cog in Daniel Murphy at second base and they have a good trade chip in Wilmer Flores at third base.