Well Berit really does seem to have had some bad experiences in Madagascar - but his criticisms represent just one point of view.
Beaches in Madagascar are not generally misused as public toilets. Sure some are - happens in Europe as well - and it certainly also happens in Indonesia, as I very well know, but a generalized judgement is completely unjustified in both countries.
Madagascar is really filthy? No. It quite definitely is not. There is no more dirt and squalor than in any other poor developing country, and no more than in many parts of Indonesia either. And the majority of people in both countries set great store by personal cleanliness and hygiene. Infections just won't heal in Madagascar???? Well maybe Berit's didn't, but mine do, always and rapidly - if I get any at all - and you don't, in Madagascar, actually see hordes of people wandering around with open unhealed sores or debilitating infections.
Indonesia is safer? Oh really? Well I find it difficult to recall the last time anyone in Madagascar blew up tourists (Bali), when different religious communities set about killing each other and anyone else who got in the way (Sulawesi, Moluccas), when the government practised something close to genocide on an ethnic group they consider inferior and killed foreigners who witnessed it (Irian Jaya) and conducted a vicious civil war against a people whose traditional independence prevented them kow-towing to the dominating ethnic group (Aceh until recently).
Madagascar is one of the safest developing countries there is. The main danger there is road-traffic accidents, but Indonesia is not a world leader in road safety, either. Sea passages in both countries can be a danger to life and limb.
It is just as easy to travel independently in Madagascar as in Indonesia. In fact on one level it's much easier, because there are no areas where travel is restricted by the government or where you're advised not to go by your home foreign ministry. Public transport in Indonesia is generally more comfortable, if that's a criterion for you, but whether or not you find taxi brousse travel in Madagascar a drag is a matter of personal attitude. In Madagascar you can get almost everywhere by taxi brousse, and I find the experience and the contact with local people always interesting. Comfortable it is usually not, but my bones have yet to be wrecked by the experience.
Indonesia is cheaper? No, sorry, but no.
Indonesia has more diversity in landscape? Well, one guy I met there said Sumatra was monotonously dark green and in Java when you've seen one rice terrace you've seen them all. It's a point of view. A rubbish one, but it reflects an attitude. Madagascar has a huge diversity of landscapes from the rainforests and beaches of Masoala in the north-east down to the spiny forests of the south and everything in between.
Diversity of cultures? No contest. Indonesia has it.
In Indonesia people speak English and in Madagascar they speak French - does any serious traveller really make that a criterion for choosing which country to visit?
"In Sumatra 'it' was simply everywhere? Well assuming we mean roughly the same thing by 'it', 'it' is everywhere in Madagascar too, if you care to look for it.
Where's all of this leading? Well really to the point that you shouldn't have to choose. Madagascar and Indonesia are not similar, except in the trivial sense that they're both developing countries and you'll find typical developing country symptoms in both. Otherwise they're hugely different and travelling in both can be deeply rewarding. And I wouldn't, by the way, let the dangers I've listed above stop me going back to Indonesia.
As right now I'm taken up with Madagascar's wildlife and biodiversity, I'm tempted to follow BigBri's recommendation and say Madagascar is "severely threatened ecologically, see it while you can." But then, what about the rainforests of Kalimantan, the orang-hutan, the Java rhino, the Sumatra tiger - you need to be in a hurry to see them, too.
The problem is, PW, you've posed an impossible question. How do you choose between two incredible countries that people quite rightly get equally passionate about? Go to one of them this year and the other next year. Perhaps as you've just experienced one South-East Asian culture in Myanmar, you should try something different and go to Madagascar first.