If anything RWD has more room for the gearbox than FWD.
The gearbox will free up over time but it wouldn't hurt to ask the dealer to check the oil level.
If they question that, point out that one has already been found with virtually no oil from the factory, after it destroyed itself.

**I posted this in another thread but I think it applies to the OP***. The transmission is Aisin and it's a very close relative to the manual gearbox in the RWD 6MT used in the Lexus IS250. I drove a 2006 MT IS250 for two years, from brand new until 2008 (approx 35,000 miles). From my experience, I have heard VERY similar noises as described by the OP. I even had the infamous "jar of marbles" sound when shifting lower gears at slower speeds. I never had any mechanical problems with the IS MT clutch or tranny. I sold it to a work colleague and she and her husband drove it another 25k miles with no issues. I'm not saying you don't have an issue to be addressed, but I can say from my experiences the tranny and clutch did have a few quirky noises in my IS. BTW - I drove that IS hard and loved every minute of it.

I have the same problem, shifting from 1st to 2nd from a cold car is occasionally difficult. I just take my time shifting and manage to get it to go without abnormal pressure. After the car warms up, the problem goes away. I will probably change the transmission fluid to one of these soon to see if it makes any difference:

http://www.amsoil.com/storefront/mtg.aspx

http://www.redlineoil.com/product.aspx?product=50304

Note that the manual specifies a 75W-90 gear oils with grade GL-3. From what I can find, GL-3 has been mostly superseded by the GL-4 specification. In any case, excellent synthetic GL-3 oil does not seem to be very available. My research also suggested that GL-5 gear oil would not be appropriate for this transmission.

thiner transmission oil fixes all these issues :D

GL-3 seems to be specified when copper/bronze are used in the box and a GL-5 spec could cause corrosion as you no doubt found. GL-4 seems to be an alternative though, from memory?
It doesn't seem to be much of a penalty, to have a tight shift for a couple of minutes, to then have superb shift quality when the oil viscosity reaches its optimum in its normal operating temperature range.

The floppy paddle shifter FR-S/BRZ uses the same IS250 slushbox as well.

I have this issue as well, do you guys think a high quality synthetic transmission oil will resolve or improve this problem?

If GL-3 has been superseded by GL-4, then why does Mitsubishi now call for GL-3 oil in the new Evo X when it used to require GL-4 in the older Evo's? The GL ratings are based on the level of additives that are appropriate for the transmission design. The higher GL ratings have more additives which can be more corrosive or too slick for some synchros. I would use extreme caution using anything but GL-3 if the manual doesn't call for it. You might get better shifting in the short term but you may be sacrificing long-term reliability.

Second gear feels off to me. It is the only one though. I had the dealer look at it and they came up with some excuse, needless to say I will be keeping an eye on it.

By doing the double clutch can solve the problem. However, try not to shift it to 1st gear while the car is still moving. It applies to all MT.

To the OP its is prefectly normally for the gearbox to feel Ike that. My IS200 is the same and I had a TRD short shifter. Which feels identically to the box in the 86/FRS. For those who don't know it's based on the same box as the IS200 but just upgraded. Similar boxes are also used in the MX5s and S15 Silvia's all have felt the same. Just do regularly oil changes and you should be fine.

Cold mornings let the car warm up before driving off and also the use of heel toe and double de clutch in the morning should see it easier to slot in.

I wonder if there is air trapped in the clutch system or just a adjustment under the dash at the pedal would fix this?

I am going to go walk out and see if the pedal travel is adjust able. Both these ideas would explain why some have problems and some do not. Since those parts are installed at the factory by people.

What the op is explaining is prefectly normal behavior for that gearbox cold. Which has been around for 14 years.

There wouldn't be any air in the clutch system it's hydraulic. As soon as there is air in the system your going to know about it.

Want to stop it feeling a bit notchy when it's cold. Start the car in the morning let it warm up. Make yourself a coffee and then in enjoy the drive :)

Ha! I tried The car is up in the air. No luck till it comes down from the lift.