It seems like someone up there is at least trying to make a valiant effort to improve QOL, but I have some issues with this one.
I don't have any heartburn with this, and I think it's a good idea. As pointed out in the article, they're trying to figure out a way to provide incentives for retention - as they've found out, money isn't everything. The Coast Guard has had a similar program for some time. It hasn't apparently impacted their mission accomplishment (Katrina), and I'm curious as to what it does for retention. My answers below are based on the assumption that the Navy's program is going to be similar to the Coast Guard one.
1) Who decides who gets to take the time off? When it comes time for a ship to leave every E-3 on the boat is going to want to go to college or pop out a kid, or care for his pet squirrel.
In order to qualify for the Coast Guard one, you have to have reached a point that you can get out. It is an unqualified resignation, with some benefits that you don't normally get when you go into the IRR. So, every E-3 on the boat isn't eligible to get out, so they wouldn't be eligible for this program. It's not like you sign up for 6 years, hit the 3 year mark and say "I want 3 years off". It's more like sign up for 6 years, hit the 6 year mark, re-enlist and say "I'll see you again in a couple of years." If anything, it's going to ensure that the depth and breadth of experience you've spent 6 years building will be back in a couple of years.
2) Telling a sailor (or Marine, airman, soldier) to only muster once a year for a drug test and a PFT is like giving a wallet with $10,000 in it to a teenage girl or a crack whore and telling her to bring it back in full a year later.
I disagree wholeheartedly with this one. Remember - it's not geared toward people who just want to get out. It's geared towards people that want to stay in, and just want a couple of years to pursue education, family, what have you. I honestly think this argument is hogwash - someone whose intent is to return at the end of 2-3 years is going to abide by it. Someone whose getting out is going to get out.
3) Some will desert. Especially the ones that had a tough life on the inside and no esprit de corps to go with it.
I doubt it. Again, it's not geared towards the bitter ones. It's geared towards those that want to stay in. The ones with a tough life will get out. Hmm, if you were a young knucklehead that had a rough life and no esprit de corps, and you can either get out at 4 years - and spend 4 years in the IRR with no requirements for drug tests/PFTs, or you can apply for 1/15th of your pay but have the drug tests & PFTs, which are you gonna choose? You're going to say "Fuck the Suck" and get out.
4) There are going to be a lot of hoops to jump through to get out on this program. So many that the people who it is meant to be for are just going to throw their hands up and say screw it.
I doubt it. If you read the Coast Guard instruction, it's an unqualified resignation. In the Marine Corps, that means a Page 11 entry. You get out with a Reserve Commission. That happens all the time in the Corps. Some people affiliate with reserve units, some don't. The only "hoop" to jump into is to submit a letter intending to return to active duty. Big deal.
Oh, and I've got a little bit of a surprise for you - this "program" merely streamlines a process that already exists in your beloved Corps. You can get out, go IRR/affiliate with a reserve unit, then request to Return to Active Duty (provided you're not a LtCol or higher). They hold quarterly boards to accomplish this. As a matter of fact, there's at least one general that did just that.