One of the major difference in the two systems is that the SIR raises the top mounting platform a little (Wes would know the exact height). Some folks feel like this will create a problem with mounting some optics to the SIR. The only problem I can see is for mounting an Eotech. You just cant mount a Eotech to an SIR and be able to co-witness the irons. With the integral mount of the Eotech, you are just limited in your mounting options. You can mount a Eotech to a RAS II and co-witness, but you will have to mount it out over the handguards. Though I have not used one like this, I think that would be the best place to mount it anyway. I really like forward mounting the dot sights I do have, and mounting the Eotech up there, you will be able to use whatever rear sight you choose to install through the Eotech. If you mount the Eotech behind the bridge of the RAS II, I don't believe you will have room to also mount a BUIS. If this is in fact true, you definitely want to get it out over the handguards with a BUIS.
It seems like most folks running Aimpionts on the RAS II will be putting them on the bridge, or hump of the RAS II. Like I said earlier, I am a big fan of forward mounting dot optics, and would rather see the Aimpoint mounted to the handguard section of the rails. While you can do this and still co-witness with the RAS II, an Aimpoint, and a correct mount, I think it might look a little goofy and uneven. Of course, when it comes to function, this doesn't matter at all, but I cant help but thinking about the hump of the BUIS, then the valley of the flat top receiver rail, then the hump of the bridge on the RAS II, then the valley of the top rail of the handguards, then the tall mountain of the Aimpoint plus mount sticking up in the air, then the valley of the rest of the handguards, then the front sight. Know what I mean?
Other than that, I personally feel there is no problem mounting any other optic to the slightly raised mounting platform of the SIR. If you use a Aimpoint, get any one of the many mounts without a spacer and it is at the correct height. Use ARMS #15 mount if you have a Reflex. If you have a magnified ACOG, you cant co-witness your sights without removing the optic anyway. And while mounting an ACOG with any of the flat tops mounts it uses, directly to a flat top, puts it at the correct height over bore, I have not a problem whatsoever using my TA31/TA51 mounted to the SIR. I thought I might, but I don't. In fact I don't even notice the difference. To be fair, I should say that I generally am not very sensitive to small changes like that, so its no surprise to me that I don't really notice. If you are sensitive to small changes like that, maybe you would notice? I don't know.
Aside from this, I will just copy and paste some text from a previous post about my feelings about the small, but noticeable differences between the two systems.
I like the fact that the SIR has removable rails. Rails are good thing to have on your handguards. But unwanted rails are uncomfortable to hold on to and they can heat up very quickly. The RAS II's answer to this is to cover the rails with panels. Panels are ok, and they do shield your hand from the edges of the rails and the heat they will acquire. But the panels are directly attached to these aluminum rails and even they will heat up eventually. The SIRs answer to unwanted rails is to allow you to take them off completely. I like that. You don't have to worry about having or losing panels, or having the panels heat up. You don't need the rail on that part of the gun, take it off.
I also like that the lower half of the SIR is synthetic, not aluminum. I am telling you, the lower portion of the SIR simply does not heat up. Period. In some testing I did, I ripped 5 mags through the SIR on full auto as fast as I could load the mags. It got warm, but no where near too hot to hold. I did the same thing to an Oly FIRSH which is another aluminum rail handguard, and it became too hot to handle. If all goes well, I will be doing the same test to the RAS II. We used a digital thermometer in these tests and will have precise figures to show people just how hot they got.
In the end, I can hear someone saying that the synthetic lower of the SIR is weaker and they would rather have an all aluminum handguard. I disagree, but not so strongly I don't want an RAS II myself! I can also hear people saying they would rather lose the removable panel of the RAS II than the aluminum rail of the SIR. Again, I can see the point, but the off chance that I lose the actual rail does not outweigh the advantage of not needing panels to begin with that I get every time I shoot the gun. Others might disagree and I don't feel strongly enough about it to make an argument.
Comparing the RAS II and the SIR is not like comparing apples and oranges. They are the same type of system. They do much of the same things in somewhat different ways. It is much more like comparing orange juice to orange juice. Which do you like better, Minute Maid or Sunkist? Pulp or no Pulp. Both are awesome systems, but do just what they are supposed to. I think each have somewhat small advantages over the other. The only problem will be in determining which of the advantages will be most beneficial to you. Once you find out, you wont know which is the better system, but you will know which is the better system for you.
Sorry for the long post. I didn't think I would have this much to say.