Okay, I decided to go through this, if for no other reason, it lets me clarify how some thing work in my head, and gives an example of what kind of thing I'm talking about.
For my example I'm going to use my namesake character, Paragon. Though he's gone through a number of game systems (and, in fact, when trying out a new SH game system with my players, I use him as the exemplar of how character gen works in the system), a version of him actually got his start all the way back in the V&V1 days (I'm an old fart). He's basically a physically augmented human who got his powers when he was exposed to an exotic bioengineering tool that had been repurposed (by people who didn't understand it) as a bioweapon; he's essentially a human body as a host for an advanced quasi-viral colony that contains his consciousness now and augments and will rebuild him any time he's injured in realtime.
I decide what I'll do is do the sort-of middle case where I use the steps listed for rolling, more or less, but pick choices rather than roll them.
First off, I decide to go through the more or less non-mechanical parts just because.
Birthplace: Paragon (Thomas Shey) was born in Los Angeles, California, in the modern period; Species: Human (sort-of); Age: He appears to be in his late 20's, though he's actually a couple decades older than that; Gender: He's a cisgendered man with the same expression as his identity, and he's a straight-leaning bisexual.
Motivation: He's primarily motivated about protecting the innocent and making up for the rest of his law-enforcement team that died when they were exposed to the bioweapon (he blames himself for this even though there's a limit to what he could have done); that's easily enough rolled up into Penance, I think.
Origin: Though he's got some rationale that puts him in Mutated (he had a minor mutation which is why he survived exposure to the bioweapon), he really fits best in Science Accident.
Power Level: For simplicity, I'll build him as a Standard super.
Basic Characteristics: Classically, his important attributes have been his toughness, strength and intelligence/perceptiveness in that order, so we assign him STR 16, END 18, AGL 10, INT 14, COL 12.
Powers: I go ahead and pick six powers, split into the usual three categories; he's got a couple of other things he sometimes does with offensive use of his quasi-virals that could be bought as poison, but those aren't a high priority, so for this version I skip them. His defensive choices are Heightened Endurance and Regeneration; his offensive ones are Special Weapon and Heightened Expertise; and his miscellaneous powers are Heightened Senses and Experience Levels. Out of these the Heightened Endurance, Regeneration, Heightened Senses and Special Weapon are the most important, so we'll call those his Core Abilities.
Before we move on to buying them, let's look at his Weaknesses. As it turns out, he's got two that have been pretty central to him in the past; his acrophobia, and the fact the conducting quality of his quasi-virals makes him very vulnerable to electricity. So we take Phobia and Vulnerability. Since heights come up rather a lot in superhero situations, I decide to call that reasonably common and give him an extra 10 CP for it. In regard to the Vulnerability, he's Vulnerable to Damage rather than attracting it, and he's only vulnerable to Electrical Energy, so that's worth 2.5 points per +2; I decide to give him +4 damage from it, yielding 5 points.
Now let's go back to the actual powers. First, I decide to look at what I want to do with the points from the Weaknesses. I could just lump them in the overall points, but I decide to follow the rolled guidelines here, and put them in his non-Core Abilities and/or his Basic Characteristics. Since Paragon has got an unimpressive Agility, I probably really want those Heightened Expertise and Experience Levels.
Heightened Expertise: I spend 10 CP here. I'd probably prefer to just apply this to melee attacks, but that's too broad for one class and not broad enough for All Attacks, so I just go with the latter instead, giving him a +2 hit chance.
Experience Levels: That leaves me the 5 points for Experience Levels, which gives him a +1 Defense and Skill bonus.
Now I move along to his Core Abilities.
Regeneration: This is almost the character's defining ability. He's essentially unkillable, and bounces back from damage very fast, unless he's damaged by something heavily cell-destructive like fire or acid. That suggests the Limited Modifier, Constant Modifier, and Heal from Death Modifier. Unfortunately, with the +5 cost from Heal from Death (since you can finish him off with the fire or acid) and the +10 from Constant, even with the -2.5 from the Limited, it would cost him 30 CPs. While that's legal, its probably more than I can afford to spend when he's got three other Abilities I want to buy. I decide I can live with him only regenerating when resting, and ditch the constant. That gives him 1 hit/round Regeneration with Heal from Death (+5, not if burned), Limited (not against fire or corrosion) at 20 CP.
Heightened Endurance: As it turns out, however, when I get to his second power, I can't spend all the 20 I want to on it anyway. He's already got a an 18 Endurance, so I can't spend more than 12 on Heightened Endurance. Given that, I just spend the 10 to bring it up to 28, and toss the other 10 back at his Regeneration, giving it back the Constant modifier.
Heightened Senses: One of the other things the quasi-virals do is function like one massive sensorium, augmenting his senses in a number of ways. I'm not likely to be able to afford all the things this does, but some have priority. First of all, he has a proximity sense, where his sense of Touch is capable of picking out motion around him by disturbances in the air so he can fight in the dark and detect hiding or invisible foes. Looking at Touch, it seems like this would be covered well just by making it Ranged (+5). It might be nice to make it a Full Sense, but I think we need to points to give him his second most important sense: his sense of smell, which he can use to track and make fine distinctions. In fact, that sounds like upgrading his Smell to a Full Sense for +10 points. Finally, his Vision operates in somewhat lower light than normal, which sounds like at least a level of Amplified sense here (+5). That uses up the 20 we have to work with here.
Finally we get to his Special Weapon. This is a custom battle-staff which normally has a built in ranged weapon. We just split the points between the two functions here. For 10 points we get a +d6 blunt attack, which is fine (he's not supposed to be all that powerful on the offense). The ranged element is a little more complicated. Normally its a laser, but I'm not going to split off into Light Control, so we'll just call it a flechette launcher and go with Sharp Ranged. For 10 points that would normally get him a d6+d8. 12 charges is more than he really needs, though; usually its more like 6 in most game systems. Hopping over to the list of general Ability Modifiers, I find this saves him about 5 CP. I also notice that the Two-Handed Gear modifier will save him an extra 2.5. I decide to use the 2.5 to push the melee damage up to d6+1, and on the ranged end, actually push it down to 2d6, but add 5 points of Armor Piercing on the darts.
At this point, all I should need to do is figure his calculated and secondary characteristic values, and decide on things like his legal status.
Carrying Capacity: 240 lbs.
Basic HTH Damage: 1D6+1 (so 2D6+2 with his battle-staff)
Save numbers: EN 13 AG 10 IN 11 CL 11
Hit Points: 25
Healing Rate: 4.5 (though his Regeneration makes it kind of moot).
Physical Defense: 11 (+1 from Experience Level)
Mental Defense: 15 (+1 from Experience Level)
Inventing Points: 5
Mass: 230 lbs; d6
Backgrounds: Education/Academia and Security/Law Enforcement
True ID: Thomas Shey
Costume: Black and smoke grey bodysuit with boots, gloves, and full face mask.
Legal Status: He would likely not have a license because he's overly leery of some of his history catching up with him. He's not exactly wanted, but there's an investigation not entirely dead about the disappearance of his prior identity (and it doesn't help that he hasn't changed his name).
So, if I'm not confused that appears to be a compete character, and I don't think I've missed any steps needed for process. As is typical, he's probably better at taking a hit (between his high hit points and regeneration) than dishing one out, but that's the way he rolls. He's also a little less mobile than he could be, but not terrible. Between his Background and superhuman sense of smell, he can be an effective investigator.