First things first, the comics make it pretty clear that Ralph is a better detective than Bruce. I don't mean to say "I'm a fan, I support a quirky character's gimmick over a main-stay," I just mean that Ralph is smarter, faster, and generally more perceptive than Batman. They're obviously the two best human detectives in the DCU, it's just that Batman works methodically and scientifically, he has trained himself to do the job well and performs his deductive reasoning through a process. He's good at what he does through mental discipline. Ralph Dibny is a natural, he doesn't even have to try. He normally recognizes complex situations for what they are at the first glance, his mind operates in a way that identifies all the potential pieces that might have relevence in potential puzzles just walking through a room, and he can instantly recall even the most trivial details to fill in the gaps when he finds more pieces to work with. In several stories, he takes on a mystery knowing both the "who" and the "why" before even beginning an investigation, only doing so to force the guilty party into revealing themselves. When he's *trying* to figure out a puzzle, nobody can beat him. Whenever Ralph and Bruce meet, there's an effort made to show them as equals in the field, but if you look at their independent efforts, Ralph is clearly on top. Shame that all this badness had to come down on him, and doubly so because now that he's in the spotlight again, he's too grief-stricken to be of any use with his talents.
As for your thoughts, I can see Sue setting up a scenario "fake doing something bad, don't let me know what it is, because invariably Ralph reads between the lines and figures it out. Surprise all of us." I don't think that was the case, however.
For one, Sue would never go so far as to fake death and to leave her own corpse. She usually gets abducted if she's involved, not killed. Ralph enjoys the fun of solving mysteries, not the danger and heartbreak associated with villainy. It's supposed to be a *fun* surprise every year, a romp. Also, Ollie knew what the mystery was supposed to be that night, and he was supposed to be in the cake at the end (anyone else notice the cake on the table is too small for Green Arrow to fit? Ray Palmer, yes, Ollie Queen, no...) Assuming the cake was meant to accompany the presents (and Ralph wasn't supposed to see either until the end), then we have the mystery *ending* at the Dibny's house, not beginning. Also, given the pregnancy, it's doubtful that Sue would take any active physical role in the mystery. She'd probably wait at the house and receive guests... so, this is not Sue's mystery.
However, the coincidences are just too great. Someone knew of the event, and hijacked it. Ralph was expecting a mystery, and he got the most heartrending mystery of his life. The irony is just too thick not to be intentional. This wasn't an "example", a random death of a random Leaguer-associate. This was a very personal, even intimate, attack. Whoever it is is probably enjoying Ralph *not* being the one to solve the riddle, it almost seems set up so that this total deconstruction of Ralph's identity is the motive...
Someone mentioned Ralphs biography (especially birthdate) being public knowledge - remember that this doesn't take place on Ralph's birthday, and if it's supposed to be a mystery Sue wouldn't tell anyone who could pass it on to Ralph what day it's supposed to happen, which is pretty much anyone, actually. So who knew? All the guests, but not all the Leaguers, plus Alfred. Calculator might have known, as the phone-call with Alfred lets us know a simple phone-tap would have done the job, but... would he really be on the phone peddling info to Bolt while the deed was done if he knew a hit was planned on a Leaguer's wife? Would he even allow that to be done, given the weight it brings down on the villain community?
It looks like microscopic-size is the key to the mystery, but the original sound that spooked Sue came from down the stairs. If it was actually Atom, he could have just travelled into her brain through the phone while she was talking on it. As it stands, if it is Atom, he'd have to enter downstairs, give her time to recognize a threat (not just a sound, but someone walking audibly, etc... when he could just go microscopic) and time to call Ralph, throw her while she's on the phone across the table, go microscopic and kill her, then after she's dead fwoosh her with a fire-throwing piece of equipment.
So we've got conflicting evidence. The physical evidence points to Ray, and since we know he's a good guy and didn't do it, we assume he was used or mentally coerced or taken over or whatever.
Ray knew Ralph and Sue for a long time. So did Jean Loring. Sue was throwing a party for Ralph, and yet neither Ray nor Jean was invited (nor seemed to even know about it.) The greater oddity is that by coincidence Ray and Jean had an appointment for *exactly* the same time as the murder. The even greater oddity is that Ray blames his being subatomic for his signal device failing, when the rest of the league had been trying to contact him for an hour. He was subatomic for an entire hour when he should have been at Jean's? That's basically an anti-alibi. Unless Jean is the mastermind behind this conspiracy, it seems that if Ray was mentally manipulated, so was Jean. So the entire affair had to be planned out from the beginning, including the attack on Jean in which she resists her attacker - but if following the trend of throwing a mystery at the best detective he can't solve, why throw a challenge to the Atom using *ROPE*, which his powers and innate comprehension of physics let him defeat so easily? If the point was to break down Ralph's sense of self, why let Ray off the hook? Apparently, to frame him.
In this sense, the attack on Batman (through Tim's dad) was successful... the orphan dedicated to making sure no other child lost his parents has let his partner be orphaned. Ralph has been caught with his pants down, and no idea who the killer is, nothing he can do to think his way out of the situation. Ray's just a patsy. So far, the only true targets have been Ralph and Bruce...
Which leads us to the whole Dr. Light incident that seems to be behind the whole crisis - Batman and Elongated Man weren't there for the mindwipe. In fact, Ralph missed it taking Sue to the hospital, and Batman *attacked* the Justice League on Light's behalf during Zatanna's mindrape thing. They are basically the only two who *weren't* complicit.
So, who would be angry at Ralph and Bruce for fighting the mindrape? Well, Carter suggested it. Ray was first to support it. Zatanna actually did it. And Barry's dead. On the other hand, Carter's a cop, Ray apparently didn't know about the murder, Zatanna's definitely not going to kill Sue over it, and Barry's dead. From that point on, your guess is as good as mine.