I think the choice of supervisor is important. Rather than basing on your judegment alone, what you could have done is actually talk to the students working there to gauge their opinion and feelings on the working environment and their supervisor.

As for writing the thesis in BM, that is not such a big deal. But I can see why some people are turned off by it. There is a way to get around it though (which I did, but not intentionally).

Check if that supervisor has a collaboration with a foreign researcher. This is also something you can ask when you discuss with him/her "is there any opportunities for foreign collaboration etc..". This can add more oomph to the paper that will be published as well as your thesis credentials.

If don't have, look for one yourself.
Then suggest to do an attachment for a while (usually 1-3 months) with the foreign supervisor. It will be even better if you ask them on the idea of co-supervising, i.e. add the foreign supervisor name to your project. In truth it will be just on paper only since you're mostly stuck on Malaysia.

Finally, you apply to write your thesis in English with the excuse of having a foreign supervisor. There is a form for this, the same form that foreign postgrad students in UKM use for their thesis.

It's actually not as difficult/roundabout as it might sound.

I did my degree and Masters in UKM. I wrote my bachelor's thesis in BM and Masters in English (cos I did an attachment and had a foreign co-supervisor). But then again my BM is considerably better than a lot of folks.

I don't think writing in BM was excessively hard, the only stumbling block is some of the scientific terms which have been designated for use in BM but it's rarely heard of. E.g:
gene expression - pengungkapan gen
multiple sequence alignment - penjajaran jujukan berbilang

However there is a list/glossary available since your friends/peers is going through the same thing.

Others are simply lifted from English:
ligation - ligasi
cloning - pengklonan

I'm a little curious how good your BM is or if you grew up overseas - since I've never heard of anyone referring BM as "Malay Language".

No, I got my Masters from the Science faculty.

You only need to write your thesis in one language - which is BM unless you're a foreign post-grad student. Or in my case, if you did a foreign attachment and/or have a foreign co-supervisor, then you can apply to write in English.

I did my Masters in bout 3 years plus, but then I went for 3 month attachment and did quite a bit of things as well. I also had to travel to Terengganu and stayed there for a couple of months to set up my experiment there and sampling.

It's not the fastest way, but I gained a lot of experience and useful stuff along the way so I don't have that much regret.

Mine was the second last batch before they introduced the paper publish requirement.

It doesn't really have to be published, cos it takes a long time before acceptance and publication. As long as you get a paper accepted, then it's ok. A cheap way to get this off is to submit to Sains Malaysiana, a local Science journal which has very low Impact Factor.