I was, sadly, one of the mugs who bought an MK4 Octavia. I had an SE FE. It was the single worst experience of any car I have ever sat in, never-mind drove or owned. It was just a horrible horrible car, riddled with technical bugs.
I do sometimes check in on the threads I used to contribute to on the Octavia forum and it basically looks like in the year since I got my car very little has changed. I would not recommend one bit that you take a chance on the MK4.
On the other hand, while my MK4 was off the road for six weeks (before I finally rejected it) I had the use of a manual Superb. I found it very similar to the Octavia in the driving of it, i.e. the size is similar, as are many of the tech-principles, but every single thing on it worked. When my Octavia was rejected I had to look for a new car, and was able to get a great deal through a workplace scheme. This did mean my choice of Superb's was limited, as not every dealer participates in the scheme, and I wasn't able to spec a car for myself.
What I ended up with was a DSG with several options added already. There was not a single manual available to me. I decided to go ahead, not having drove an automatic for about 20 years, but I can honestly say I am glad and actually am finding my driving experience has only been massively improved through going to a DSG box. I would strongly recommend you consider a DSG. You still have the option of using it as a manual, and I often do while descending steep hills, as I do tend to find the car puts itself into low gears with some enthusiasm and for me I find it revs too high during descents, especially long descents, so I usually take over manually in such circumstances. For all other use I am happy for the DSG to control the gears.
As far as the tech goes, I can assure you that in five months of ownership I have not had one single problem with this car, nor did I with the loan Superb. I repeat, not one problem. Contrast that with the Octavia, where I had reported faults back to the dealership within my first month, which continue until I rejected the car five months later.
Mechanically, I guess as I have only had the car five months (from brand new, 0 miles) I will leave it to someone else to comment on that long-term, but put it this way I haven't had to contact the dealer about any mechanical issues experienced so far.
I genuinely can say that this is the best car I have ever owned, hands down, so I can do nothing but recommend one.