Re C&C spot checks - I don't see why Clerics shouldn't be perceptive. The C&C Cleric needs a lot more XP than the pre-3e Cleric, and they have fewer and weaker spells than in 1e, there's no harm in them being good sentries. They can't sneak around so they're not great scouts. Where did this idea that Clerics were blind as bats come from? The stat is called Wisdom, not Willpower or Faith. Perception is reasonably part of it.
I never said Clerics should be blind as bats or obtuse. Sure, maybe a cleric's Wis helps him with perception. And maybe a magic user's intelligence helps him with perception. And maybe a ranger's training helps him with perception. Heck, maybe a Fighter's wisdom helps him in combat. Et cetera.
My point is that I like class-based systems to use and reinforce the archetypes. And I don't consider "very perceptive/ambush-detector" to be part of the "cleric" archetype in the same way that it's part of the ranger or thief archetype. Intentionally or not, C&C makes "tends to be very perceptive" a built-in feature of the cleric class.
[Incidentally, I think it's good that C&C upped the XP requirements for the cleric, because even 1st level C&C clerics kick major ass. With their armor and hit points, they're solid in combat. They're among the best at avoiding surprise and also good at general perception (because of their high Wis which will invariably be Prime). They can turn undead. At first level, they can cast spells like the first level
cure light wounds. Not only that, they can also cast spells like the first level
sound burst, which does 1d8 damage (no save) to all creatures in a 20 ft diameter circle centered up to 50 feet away, also stunning those creatures if they fail their save. (No magic user? No "big gun"
sleep spell? No worries, mate, I can nuke those goblins with a spell that makes those pointy-hat 1st level wizards green with envy!)]
The attribute mod is not a big deal in C&C, and Rogues will typically be a level above Clerics, so the Cleric won't necessarily be the best spotter anyway.
By-the-book, I don't think level is added to surprise checks (e.g. see the "EXAMPLE OF PLAY" at the end of the C&C PH -- Suryc and Bjorn aren't adding their level when they make surprise checks). However, let's assume that you're house-ruling this and adding level in some or all cases. For the sake of argument, let's say the Rogue is Wis Prime. As you say, the Rogue is typically going to be a level higher than the Cleric, so he'll get a +1 bonus that the Cleric won't enjoy. However, it's also true that the Cleric will typically have a higher Wis attribute bonus -- maybe a +1 higher than the Rogue, maybe more. It's true that attribute mods aren't as significant as Prime/Not-Prime, but the small attribute mod is likely to cancel out the small level mod.
The fact is that Clerics in C&C tend to be good at perception because they're always Wis Prime, and they tend to have high Wis stats on top of that. It's not necessarily bad or wrong, it's just not how I like Clerics (i.e. all clerics as a class or archetype) to be modeled.
Re saving throws - I don't like looking up saving throw tables, and C&C's use of attribute checks as saves is a godsend for me. YMMV.
If you write your saving throw target number on your character sheet, there's no need to look up anything. It's no more difficult that looking at the character sheet for the appropriate ability mod.
Again, my complaint against C&C saving throws isn't that the system is necessarily bad or wrong, but that it completely throws out the importance of your character class, and it models the saving throw much more like a "resistance roll" heavily based on the stat. That's just not the way I like saving throws to work. I like class to be the most important factor in saving throws, and I don't like them to scale perfectly in tandem with the threat level. It's not *wrong*, it's just a completely different approach from traditional old-school saving throws, which I prefer.