1. The OP asks how this comparison would work Halachically?
The simple answer seems to be that the question is not a Halachic one. Halachah is the body of laws that tell a Jew how to behave in thought speech and deed. Halachah usually does not comment on comparing people in judgment in the eyes of Hashem. If it does, it would only be in passing as concerns a Halachah. For instance, one who violates the Sabbath publicly or worships idols would not be accepted to ritually slaughter kosher meat. Someone who wore a suit made of wool and linen, could still slaughter kosher meat. Doubting the resurrection of the dead, etc. does not seem to have such a Halachic effect.
Halachah would simply say that a Jew should both believe properly and act properly without sacrificing either goal. :)
This is more of a question on Hashkafah (Jewish moral outlook) and Kabbalah (The secret system of how Hashem runs the universe etc.).
2. The OP also asks if this man with doubts who performs mitzvos would be lesser or more pious in the eyes of Hashem than one who believes but lacks as much observance.
The answer is that no person could really be the spokesman for G-d on this one. Tehillim 33:15 is quoted by Chazal regarding the day of judgment. It says that Hashem is the one who fashions all hearts and understands all the deeds (of mankind).
Hashem takes everything into consideration when judging a man. This includes his upbringing, opportunities in life, conditions of life, his intelligence, ability etc. Therefore, even two people who equally doubted the resurrection of the dead but observed the laws, would be judged differently! It all depends on each person's abilities and challenges. One man eats pork while another man comes late to prayer. Who is better? The answer is that no one knows. It depends on each person's level. You may wish to read Rav Dessler's "Michtav M'Eliyahu", where he discusses each man's "Nekudas HaBechirah". That is a discussion on each man's level of free choice regarding different challenges.
So the answer is that we really do not know.
But, in general, Pirkei Avos ch. 1:17 (quoting Rabban Gamliel's son Shimon) does say that the main thing is the "deed" (not the "learning"). Man can certainly struggle with the whys and whats of Judaism intellectually. However, it is the disciplined man who acts properly that trumps knowledge by itself.
Finally, 3. it seems to me that the OP is implying that it wants to know what is "so bad" about doubting the resurrection from the dead and other Messianic age promises or; at least, we could intimate that the OP wants to know "how bad is it" to have doubts about this? (in Judaism)
Tehillim 92:7, "An unrefined man does not know, and a fool does not know this..."
Why does the pasuk repeat the example? Why does a boor simply "not know" but a fool doesn't know "this"??
Two men enter for a tour of the cockpit on a jetliner. Neither man has any background in aviation. One sees all the buttons and dials and says simply: "WOW"! The fool, sees the same thing, and notices a big fat green button on the ceiling. He asks: "Why is that green button there?" The pilot laughs. "..And the rest of the buttons and dials....you have no problem with? Is it just the green one overhead that looks out of place to you?"
The fool doesn't know "this". The truth is, he doesn't know anything. :) If he has no problem with the other buttons, then he should have no problem with the green one either.
So our pious Jew in the OP example understands and believes everything? The creation of the world, the 10 plagues, the splitting of the sea, the fire descending on Mt. Carmel by Elijah, The Jews surviving Haman, Antiochus, and Hitler, then thriving as a nation today, and returning to the land of Israel etc. etc., ...these he has no question on. G-d can do anything. But G-d can't, or won't, return a pile of dust to life? He will not tame a lion so that it won't eat a lamb? He can't convince some people to believe in Him? "This" is the issue??
Talmud Sanhedrin, chapter Cheilek, 91a: A certain heretic once said to Geviah ben Pesissah (a Rabbi): "If even the living must die, then the dead should certainly remain dead!" Geviah answered: "If people who never existed can live, then people who once lived can certainly live again!"
The mistake the example pious Jew in the OP is making is a lack of "emunah". The particular lack is that he never internalized the fact that Hashem created and runs the world from nothing to what we see here, today, constantly.
Hashem made a world from nothing. There is no reason to believe that anything created by Hashem should be able to be destroyed? Yet things die and break. That is a miracle and Hashem's guidance. So too, when He decides to resurrect the dead, it will be a miracle and His guidance. How did He make dirt live? The same way he made nothing into dirt, and dirt into Adam.
Lions decided to eat flesh instead of grass. Cows eat grass instead of flesh. Why? Hashem designed it so. If lions start eating grass instead? Hashem decided so.
People who worship idols or don't believe in any religion, now lack the knowledge or stimulus to change. G-d will increase knowledge and revelation to the world; then, more people will believe.
His bank account was at 1 million and now it is down to seventy five thousand. Now, it will go back up to ten million. Why? G-d runs his bank account.
This is what needs to be internalized as a first step in understanding "emunah" (trust and faith in Hashem). The person proposed in the OP lacks an understanding of simple "emunah". That is how bad the problem is. I think that once a person understands this and internalizes it, the problem is solved.
A chasid once had the following conversation with the Tzemach Tzedek (3rd Lubavitcher Rebbe).
Chasid: Rebbe, I have doubts in Faith.
Rebbe: So what, who cares.
Chasid: But Rebbe! I am a Jew!
Rebbe: Oh OK. If so, then there is no problem. :)
If the guy goes to shul and offers "honor" service to Hashem, but has doubts. Then there is a lack of real "emunah". If the Jew cries out that he believes Hashem controls his life and the world and wants to see Hashem in his life...then the doubts are already answered.