First off, this is the first of your episodes that I have listened to. It caught my attention because I am one of the contributing writer/editors for the semi-official and game developer encouraged "The Eye: Eclipse Phase Fanzine." I contributed writing to issues one, two, and, in a small way, four; and, was on the editing team for the first three. I intend to do more of both in the future. The fanzine can be found at the Darkcast Wiki. www.firewall-darkcast.com/
I'd like to address some of your concerns with the skill levels first. For one, if you read the character creation section you'll find that no skill can be raised beyond 80 at character creation unless you use the "Expert" trait, and if you're going for a "regular person" level of play you can limit the number of customization points available to the players at chargen. Yes, this can still be abused with the use of various pieces of gear and such, but allowing that, or not, is within the GM's purview. Secondly, if you are not playing a one-shot game, which you guys were, stacking one skill or skillset will gimp your character in the future. Leaving huge holes in your abilities can REALLY hurt you in the long run. The intention is to try to build a character that is very good at one thing, while still balancing them enough to survive long term. Dying gains you no advancement as the character must then be resleeved from a backup, losing all the Rez points you might have earned for advancement. A gimped character could easily become a dead end, never really advancing at all. Whether you consider this a flaw of the game system, or a "check and balance" on chargen abuse is up to you, I prefer the latter.
Next, as you noticed, Eclipse Phase gives you the default hook, for first time EP players, of having the PCs employed as Firewall Sentinels. While some might find this boring, (ahem) I consider it far superior to the "So, you're all at an inn/pub, when suddenly ..." intro so common to some unimaginative GMs. And, as noted by two of you, it is a good way to introduce the players to the main theme of the entire setting, namely, "Defending the last remnants of humanity from existential (i.e. extinction causing) threats, by any means necessary." It also explains why the PCs are NOT the "Average Joe Blow" on the street. They have been chosen for recruitment by Firewall because of their exceptional skills, resources, and/or station in life. This applies whether the PCs are already Sentinels or this first mission that they've been hired for is a test before induction into the secretive organization. Having one of the PCs being a Sentinel and the others in the dark is also a good ploy if you feel you need to inject a degree of paranoia, hint, hint. Though if you check you'll find paranoia aplenty just in the fluff on Firewall and the "Why was I resleeved? Did Firewall kill me? Accident? etc." aspect that is widely available in the game, starting with the opening fiction "Lack." Not to mention the many other possibilities (as a quick example: How many forks of me are there really? Are any of them plotting against me?) And yeah, with a game setting this detailed, starting off with "You all just happen to meet, then something happens, now jump in the sandbox and get busy," is not really the way to go until the characters are more familiar with their capabilities and the options open to them in the setting; which, I think you probably noticed.
Moving right along ... I can see your objection to the level of bookkeeping necessary. I don't have a problem with it, but I can see your point if you prefer systems with quicker chargen and simpler, less detailed mechanics. Such systems do have their benefits. Keep in mind, however, that many of the developers used to work on Shadowrun, which is number heavy. EP is intended to be a more streamlined, faster playing Sci-fi game, which I think it is; even if it is a bit number heavy on the front end. Many of EP's diehard fans, like myself, don't really notice the added bookkeeping because we migrated to it, from Shadowrun, along with the developers. Mostly because we like their work and chatted with them on Dumpshock before EP ever existed.
Also, keep in mind, there are a number of supplements available at EclipsePhase.com that can make the whole process easier; including a character sheet available just for the Ego, and a separate sheet for their stats when sleeved into different morphs. This can make keeping it all straight simpler, and I feel that the extra work is worth it if you're going to play more than just a one-shot. When I run an EP game I'll even go so far as to have the Players create multiple PCs each during the first session, giving them a "pool" to draw from and customize the team for different types of scenarios. But, as I mentioned, I don't mind the extra bookkeeping.
Now, you guys mentioned what you called a "disconnect" concerning the difference in fear factor and "otherness" between the player's perceptions and those of the PC. While you may have a point, I feel that there is a big difference between having a conversation with your neighbor, Bob the uplifted octopus, and the psychological trauma of trying to avoid being torn limb from limb and eaten by an Exsurgent virus infected monstrosity, or worse, becoming infected by it. Even we can become inured to things like extreme body modification, they've just had more practice. But life and death, is still life and death, even if you can be resleeved. Being resleeved from a cortical stack means that you still carry the trauma of experiencing death. And, the "lack" from being resleeved from a backup can have seriously alienating and dehumanizing effects on a person. I think the psychological Trauma and Hardening (becoming cold and disconnected, while also losing Moxie Points permanently) mechanics deals with this quite nicely. If you play more than a one shot I think you would get a better feel for it and that may ameliorate your concerns a bit. Keep in mind that just the "wrongness" in the appearance of the Remade morph (represented by the Uncanny Valley negative trait) can have a serious off-putting affect on many EP NPCs if properly handled by the GM. The people of the EP universe are still in the transition period before posthumanism, they're not entirely immune to the extremes of the "normal" world around them, especially bio-conservatives. Really, it comes down to your ability to subsume yourself in the roleplaying challenge.
But hey, these are just my opinions; and, nobody really listens to me.
Anyway, I like your show. I'm mostly a Sci-fi type, so I'll probably follow you all and give you a listen when you do shows in line with my interests as well as general RPG subjects. I registered for your forum, and I'm looking forward to possible future shows and forum free-for-alls. Good luck, happy gaming, and I wish you great success.