I've done both, with kids, and we like both. I personally like Vietnam more. We've travelled from Hanoi to Hue and on to Hoi An and back (that was a week in October). We had a 2-bedroom apartment in Hanoi (Somerset, but try Ascott and Fraser Suites as well, same goes for HCMC), in smaller places we always have 2 connecting rooms (2 adults and 3 children). Check Victoria hotels with several properties (and kids club) in Vietnam We've done HCMC on the way back from Cambodia and I've been back with girlfriends as well. Kids liked it, we didn't do kids things necessarily but did to the water puppet show, beach and look for places with pools to relax.
We've been to Kota Kinabalu with the kids, but that's more a beach break. I've been to KL twice, Penang and Langkawi pre-kids (the latter as a kid myself when I was 18 with my parents ... only 1 5* resort at the time!).
Both countries are fairly easy to travel with some small children. You could do Langkawi with stop in KL (and a side trip to Malacca). KL should have service apartments as well for short term stays and they make you more flexible especially when bringing your helper. Another option is go straight to Penang, and some cultural trips on the island. The beach isn't fantastic though, but everything is fairly easy.
My youngest were not even 3 when we went to Vietnam (2 when we went to KK) ... Plenty of choices.
We still want to do Phan Thiet / Mui Ne from HCMC one day ... it's quite a long drive though from HCMC (around 4 hours).