Oh I agree it took a boat load of karma, you needed the initiative enhancements (overclock), the bioskill wires, and I think it was centering, and netfoci widgets maybe it was something like that; like 6ish submersions. But we got one at the end of 4th. When a character died and the player started their new character with group karma average. Yeah it was lot of Karma, but it was effective even vs fairly deep initiated mages. Part of the issue was the lack an real sort of non-TM hacking opposition at the time, and as i recall deep submersion just wasn't as deadly as astral questing. But combined with the sort of thing you could work up with basically near perfect information from deep submersion, or just being the unspeakable god of googling stuff, a small army of sprites and the super skill build it just crashed stuff. I accept your point that it's adaptive, but it was way strong and certainly on the same scale of game breaking as several things we got out FA.
Then yeah, it sounds like your experience was an artifact of the way your campaign was structured. Less the TM being overpowered, and more the GM not being able to use the tools available to deliver an adequate challenge. I expect you would have had similar problems with any high-level hacker who had started in such a situation. Again, going back to my baseball analogy, your GM hung a curve ball high and over the middle of the plate, and the TM player took him for a ride. I remember one time I, for fun, did up a mage character (possession tradition) in 4e starting at 300 karma after chargen. To say he was able to stomp most 'street-level' challenges without trying would be a tad bit of an understatement. Immunity to Normal Weapons when you have a F12 Spirit riding your body, Channeling, and other joys made him able to ignore anything lighter than machine guns, pretty much, and even then he was able to shrug off a lot of damage with his worn armor and an Armor spell sustained on a focus. And... well, I could go on.
Actually, what you had is a common issue when players start a new character at high levels. To switch to a D&D analogy for a second, yes, a Fighter that has started at Level 1 and risen to level 15 through the campaign should be about as powerful as a Fighter that starts at Level 15, the truth is that the older character will not be as focused as the new character. Their skills will be based on what they needed as they fought through various dungeons. They may have feats that seemed good at level 6, but haven't proven to be too useful later on. Their gear will be based on what they found as loot, or were able to buy in shops.
The new character, on the other hand, will be a master of their craft. Their feats and skills will all be honed towards a certain goal, even if those choices would have been less than useful at low levels. Their gear will be just what they needed, rather than what they could find. In other words, a character starting at level 15 will likely feel stronger and more focused than one that has fought their way up.
To return to SR 4E as an analogy, someone starting at, say, 200 karma, with whatever the GM feels is a reasonable amount of nuyen to give them, is going to be in a much better situation than characters who worked their way up, regardless of archetype. A Sammy starting that high will have more Betaware, higher grade wired reflexes, and so on, stuff that, yeah, they could have gotten in a long campaign, but they would have had to save up for and then had a couple months of downtime to recover from, even after they tracked down someone willing to do the work. A mage will have more initiations, more spells, more foci. A Hacker will have a better link, more programs, more agents. A Face will have more contacts, more fake SINs, and so on.