Very good analysis except I think you ignore one major problem-----offense. An infield of Beckham, Alexei and Gillaspi is good defensively but weak offensively. Take away Paulie for probably a couple of AA prospects and you have a huge hole at first.
This team needs several more guys who can hit like Rios has the past 2 seasons. Management is going to have to open up their wallet to free agency. Maybe Viciedo moves to DH if Dunn can be dumped but that would leave 1st, LF and catcher where you need to add starters w better than average offensive skills. The other options are bring players up from the minors( good luck with that) or trade away some pitching ( which I agree looks solid) to get some instant offense.
I am ignoring the option of trading Paulie, dumping Dunn and being a bad team for a few years with the hope of building a better farm system.