I thought I'd weigh in on this one as a long time 125 guy...
I haven't owned an aluminum framed CR but I have ridden a couple and owned a few predecessors (not just my 87. I don’t know how to change that…). I currently have a 2001 yz125 and have had a couple YZ dating back to the 80s; their 250s were much better than the 125s back then, but times have changed.
Honestly, I don’t think the CR is quite as good an overall package, but it is a quality bike and can be made to work. A LOT depends on your planned use; do you want to be competitive on the local race circuit or are you play riding w/ friends + hitting the occasional track day? Though my rides on the newer CRs gave me the impression that they are a little tougher to keep on the pipe, they are NOT slow bikes. Beyond that, they are very well balanced bikes for starters. The suspenders feel good, they really handle great; from high speed straights to slam-bam bermshots and the Honda quality and detail is top notch. Things fit well and wear well. If you are getting a good deal on the bike and it is in good shape, etc., I think it is likely you’d be happy w/ it.
A similar year YZ would be a great package but my opinion is there will be a few trade offs… While the YZ has a GREAT 125 motor, a stable and decently suspended package, I do think it lags behind the CR in overall feel, the brakes are adequate but don’t have the feel of the CR (I added a CR routed brake line and it helped a lot!), the plastic seems to age pretty quickly… and overall, just doesn’t quite have that Honda crispness and open ergos. Still though, a solid bike w/ a winning motor. That said though, my buddy’s 02 KTM’s motor flatout rips my YZ (which is always kept fresh, procuit pipe, boysen reeds/cage, etc.) Handling, suspension and ergos are different than what I am used to, but that thing is a quality bike w/ LOTS of trick parts on it stock.
Every bike lacks in some areas and excels in others… Bottom line, I think the CR will treat you right and you’ll have a lot of fun on it.