The classic answer : What's there not to like ?
A number of things that you did not mention. But let's roll this up:
Ottoman Empire was on the decline and sultanate was becoming a toy in the hands of a developed and sophisticated Europe.
There's little I can bring up against that, that was no doubt the case.
It was obvious that it was planned to share parts of the Ottoman Empire in the World War I, which led to the disgrace that is Treaty of Sevres in 1920. No need to get into the the details of it assuming you already know about it.
I have indeed studied the Treaty of Sèvres intensively, and can only admit that it was an incredibly imperialist and even racist act towards the Turks.
Mustafa Kemal Atatürk started the independence journey back in 19 May 1919 in the city I was born and now living in, Samsun. He managed to gather around the Turkish people to save their honour and regain their independence. We managed to that in the Turkish War of Independence.
Pars pro toto, I'll get into history a bit here. No doubt the war was a matter of honour and integrity for the Turks, but have you ever tried to look at it from the perspective of the opponents the Turks were fighting at the moment? Just as the Turks were humiliated by the course of the First World War and the Treaty of Sèvres, the Greeks still felt humiliated by the centuries of Ottoman rule and the loss of territories that had belonged to them. The Armenians had never known such a thing as national independence in modern times. I understand that to the Turks fighting against them, the Armenians were traitors because they allied with foreign powers to fight against what in the eyes of the Turks was their own country. But they didn't fare particularly well towards the end of Ottoman rule, and in the end you will ally with anyone who promises you what you want.
But I'm not going to fall into the cliché of an European do-gooder and argue against Atatürk on the grounds of his politics towards the Greeks, Armenians and Kurds. I am sure you have heard it all, and that you are tired of it.
But building upon the ashes of a miserable Ottoman Empire to create a modernized republic is unbelievably fascinating.
What happened in Turkey in the 20s and 30s in terms of modernisation is indeed quite impressive. It is certainly the merit of Atatürk and his surroundings that he managed to use the scant resources available to him to maximum efficiency. In the wars, he has proved himself a capable military commander - perhaps the only one at Ottoman and Turkish disposal. I will not doubt that it is an impressive trait to successfully transfer your military abilities to domestic measures.
Atatürk believed in science as upposed to Ottoman Empire's beliefs in religion and mandate.
I think it is a cliché predominant among intellectuals in many Muslim countries that it was strict religiosity and traditionalism that kept them from advancing. The Ottoman Empire was crippled by a decline that had begun two centuries before the First World War, when it was still a relatively modern state that more or less kept up with the developments in Europe. I think that many factors contributed to the initiation of this decline and its steady process, including the hostilities between Ottomans and Europeans, the overstretching of Ottoman resources, the almost constant state of war against Austria, Russia and Persia, and the immense heterogenity of the Ottoman realm. Just how are you going to keep an empire together that is so diverse enough to include metropolitan areas like Istanbul, isolated rural regions like the mountains of Kurdistan, intensely irrigated Mesopotamia and the pastoral Balkans? All that spread between Algeria, Yemen, the Caucasus and the Puszta? It's bound to fail.
Naturally, the regressive nature of the Ottoman Sultanate did not help the situation very much, and an emperor who prefers to donate to Mecca instead of taking care of imperial infrastructures does not have his priorities straight. I'm not saying religion did not play a role, but it was far from being the only one. I think the main reason for Ottoman decline were the closed doors towards Europe that prevented the Ottomans from catching up with industrialisation. When the sultans did see that they had to do something to modernise their country, it was obvious that the Europeans would only share their secrets for a high price. But did that make the Ottomans puppets of the West? If yes, then how do you explain the costly wars against Austria and Russia, or the terrible choice of alliances in the First World War?
He created the first foundations of researching in history, culture, geography etc. in a modernized fashion.
This is one of my biggest beefs with him. I don't call it a "modernized fashion", because it was really a nationalistic fashion in a time when he could already have known it better. Historical research is worthless if it is done under an ideological banner, whether you call it "modernistic", "nationalistic", "Kemalistic" or "Turanistic". I know that Turkey is far from being the first or only country to have historical and cultural studies undertaken under the premise of nationalism, but that does not make it good or correct. I have witnessed Turkish students trying to interpret virtually everything of importance in cultural history as something inherently Turkish. The proof, if existent, is usually outrageous, such as a passing resemblance in Turkish and Celtic grammar that any serious scholar can prove to be coincidental. Again, this is not a purely Turkish thing - Iranians love to do things like that as well - but it is not necessary. The science and scholarship introduced under Atatürk was already outdated, almost old baggage that European universities were glad to drop off.
Not to mention the modern clothing style, the modern alphabet,
And here, "modern" means "Western". I find it ironic that you call out western influence when you don't like it, but don't lose a word of it when you consider it "modern". Of course you can say that introducing "modern" clothing is a good thing, but it went hand in hand with banning the fez and the veil, which stands in stark contrast to what you said about people being able to choose their own religion. I know the intention Atatürk had with it was good, in the sense of abolishing old and regressive traditions that in his eyes crippled the country, but I find that banning something is not the optimal solution, and certainly not the democratic one.
As for the alphabet, I wonder if it really did more good than harm. Introducing the Latin alphabet was really just the most visible aspect of a radical and unnatural language policy. The Turkish language was "pruned" of all words and sounds that were deemed "un-Turkish". Arabic and Persian words were replaced by ones that were perceived to be inherently Turkish, and taken from a study of ancient and contemporary Turkish languages spoken in Central Asia. Phonems such as the qaf and gheyn were abolished completely, and the Arabic script was banned. The essential consequence was that any text written prior to the age of the Turkish Republic gradually became unreadable and unintelligible to anyone but scholars specifically educated in reading them. The Turks lost access to the sources of their own history. Have you ever wondered if those Ottoman manuscript may say something other than what you were told? How are you going to find out?
So I'm not going to say that Atatürk did not do a lot of good stuff for your country, but I think that many of those policies related to culture and education were wrong (plus others which I said in the beginning I won't get into). One of the most pivotal necessities of a civilised country is self-reflection. A country needs to be able to look at itself critically, look at its past and re-evaluate its own perceptions of triumphs and wrong-doings from time to time. In a democracy, this is the duty of any educated citizen, no matter what he is trained for. History needs to be read critically and evaluated critically. An official version should never be believed until you have other, independent sources that confirm this picture.