Vermaelen
Jones is a good transfer, up until TW2 at least (when Vidic returns). Whilst I think the Old Trafford drubbing will have shocked Arsenal into pulling themselves together, along with the good signing of Per Mertsacker making them more sound in the middle of defence, making Vermaelen still a decent SDT pick (the Sun love him), I feel Jones will have the majority of Vidic's absence placed in his responsibility and, playing at Man U, will continue to pick up the points for 1.5m less than Vermaelen.
Gardner
Mata is also a good transfer. Whilst he is a CK, Mata is far too good a value midfielder playing for a top 3/4 club to be ignored, and has already got a Premiership goal under his belt. I'm confident he will continue to ease into the left slot in attack past Malouda until he's well and truly first-choice. That is why they paid £23.5m for him after all. We can, and probably should, have him for £20m less than that.
That leaves one transfer left, which, I would agree with you, should be used on Nani. However, I'm wary of agreeing it should be in exchange for Hernandez. Whilst I think he is a fantastic player, I'm worried he does little, being such an out-and-out striker, to earn those important 7s in losses, draws or even scrappy wins. Having said that, being the furthest option up the pitch should mean goals. But you do already have Rooney. I would perhaps look at Aguero or Dzeko at Manchester City to spread your point-scoring potential (i.e. if Manchester United have a bad day- not a common occurrence, granted- you can hope that City and/or Liverpool have better ones, with Aguero/Dzeko and Suarez bagging respectively).
One draw to this is you're likely to see Mata, Aguero and Dzeko top, or near the top at least, of the '% transferred in', meaning your team will have fewer distinguishing features points-wise (though at least you won't lose pace when they score heavily), whereas Hernandez is actually being transferred OUT of a lot of teams (another post somewhere showed the current table, but it can be seen at any time on the Sun's website), which would make your third transfer pretty nifty should he start to score big.
Other alternatives to Nani that may not be as 'popular' as Dzeko/Aguero could be Ashley Young for £5.5m or Theo Walcott for £5m. The former I believe will still be quite popular, but I have a hunch the latter could be shrewd, as I feel he may be tasked with getting a fair few of Arsenal's goals now that Fabregas and Nasri have left.
Strong team though, solid start I'd imagine, so well done and good luck for the remainder of the season. Or until TW2 at least!
No need to do anything cavalier/stupid.
