I think the Malaysian ladies are at a much better shape than our Indonesian ladies right now. At least, Wong Mew Choo is showing that she can compete at the highest level and she's still young isn't she? Wong Pei Tty and Chin Ee Hui have performed consistently over the past one year and I would rate this pair as equal to the other top South-East Asian pairs like Saralee/Satinee and Jiang/Li.
For MD, Malaysians do have the advantage of numbers. I count at least 2 young pairs who can make the mark and are already in the top 20 now (excluding Chan/Koo). These 2 pairs are Tan Bin Shen/Ong Soon Hock (20 and 21 years old, WR 11) and Mohd Tazari Fairuzizuan/Lin Woon Fui (WR 14). With Rexy's help, these 2 pairs can only be better in the future.
Of course, not to forget that there is another pair Gan Teik Chai/Abdul Latif Mohd Zakry who is ranked no 19 and last year's world junior champion , but this pair is still inexperienced. So, 5 pairs to rely on for the next few years...not a bad sign after all

As for Choong/Lee, its a good idea to have them as a sparring partner to provide the experience, but, they only have at most 2 years left.
The most worrying must be men's singles (same as Indonesia). Lee Chong Wei is improving, but, he's still not a great player. Besides him, only Hafiz Hashim could be counted as a top player. Kuan Beng Hong is probably a player for the future....but others???