Yes and no, say some comparison videos that hit YouTube yesterday. In the startup (above) and DVD loading, you see the Slim marginally trails the Phat. But in starting and loading Batman: Arkham Asylum, it's faster.

http://kotaku.com/5348819/is-ps3-slim-slower-than-ps3-phat

well as stated in many of my posts generally when shrinking a PPC die you run into many problems, and the chip normally ends up running faster unexpectedly (even outside of any predicted), IBM tried this time to keep it clock per clock the same (10-20% improvement on the same design not unusual). this means they actually slowed down the die shrunk chip while working on it, this was to maintain how games ran on the PS3. no doubt this was hard to do, and could cause irregularities in certain functions. when they tried to control this in early generation IBM PPC chips make power2-3 run at specified clocks, they inadvertently caused the first batches to run 50 mhz slower (this is back when 450mhz would have been the fastest cpu on the market )

edit, as a note, you do not want one console running faster or slower from the same family  generation series it causes problems in game play and eventually can render games unplayable 

Well, that sucks.

Hopefully this isn't that noticeable of an issue, and sticks only to loading times.

Phat FTW though.

looks like the same speed to me...

different firmware guys.
neither have 3.0 version yet.

Wait till a couple of them break.

It doesn't look like it will make much of a difference.

Wouldn't the bigger HDD cause longer seek times? not the chips.

Not necessarily, the harddrive specs could be different other than size. For instance my old 500GB had an average transfer rate of about 80MB/s and 13ms seek time, while my newer (and now full) 1TB drive has  an average rate of 95MB/s and average seek time of 10ms, both are 7200RPM drives but the TB has a larger cache and some other different mechanics.

And in the case of loading DVDs and most games you do not use the HDD.

it could, especially when going form a 3.5 to a 2.5 (i believe the slim uses the 2.5 but you can correct me if im wrong) however, far more important are drive specs, if your using a drive that is equally speced in seek time,  cache size ect you should not see any difference.

there are many different things that may or may not cause it, as pointed out in the article there seems to have been some revision in launch\boot sequence that could cause it. but until they are the same i error to PPC chips which have a know problem with die shrinks