They do upgrade and iterate the aircraft. The F-15 is up to version D/E ( E being the strike variant, ground attack roles are often added towards the end of a fighter's lifespan )
Unfortunately, there does come a time when, depending on the intended use, upgrade and iterate does not work any more.
For aircraft like the B-1/B-52 and like the A-10, I am in much more agreement with you. But for fighters, things get different.
You can do what the Russians are doing, buy many less expensive aircraft. But you have to buy more. Expense can still be high.
When the F-15 ( Design from 1967, First Flight 1972 ) entered service, 20k pounds of thrust per engine was norm, now, 40k pounds of thrust, with vectoring thrust is the norm. You say, shore it up, make it stronger. Sure, but then you really have to re-engineer a fair bit of the aircraft. Low observable was just on the horizon at that time, so the aircraft shape is not optimal, they did not have the resources to refine the shape. More re-engineering. And there are improvements in the radar and avionics. Often, existing aircraft are updated with these, but at some point the space and power and aircraft shape requirements mean it just wont go.
So, my prescription would be
update and iterate as needed
when a new aircraft is really needed, design a specific aircraft for that role. The F-22 had it's teething pains ( if you watch closely pretty much *every* aircraft does. Famous example, P-51 Mustang. Almost didn't make it. The British stuck a Merlin engine ( with 2 speed, 2 stage supercharger ) replacing the Allison single stage supercharged engine* in a test aircraft sent over for evaluation ( the Mustang was built for the English ) after they tested it with the Allison, and found it lacking. Today, everyone forgets it's teething troubles, and praises it )
Where things go really sideways is when the aircraft is designed for multiple missions.
We keep thinking we are being smart, but it keeps biting us in the bottom. F/B-111, is an obscure example.. Supposed to be a naval fighter and ground attack aircraft. When it's role was finally limited to the ground attack part ( with the F-14 emerging as a fighter to take that role ) it was able to succeed.
The F-35 is our recent example. It may turn out to be an excellent aircraft, but it is going thru it's teething time now. And trying to make it a good fighter and bomber, and STOL/STOVL aircraft ( to suit Marines and British interest in a Harrier replacement ) is complicating things.
Separate the concerns. And, in a sense, they are, with the A/B/C variants of the aircraft, but the ties to each other complicate things.
* the Allison engine was a good engine, it was crippled by the supercharger. Army Air Corps people did not believe there was a need, never mind what was going on in Europe. The same engine, turbocharged, in the P-38 gave America it's first 400+ mph aircraft.