Well, I think we need to first define what we mean by progression. I think both system do have progression to them. The trade up system forced you through the rarities because that was how it was designed. The crafting system seems to simplify the progression by simply showing your progression by the amount of fragments you have. The later form of progression seems to me to be not as interesting to some players. I agree it is kind of boring to just see a number keep increasing.
That is why I would suggest changing the fragment amount to a bar much like the level bar we already have. Maybe have it change colors depending on what the highest card rarity you are capable of making at the moment. I think this would make the system a little more meaning full to some players.
This of course does not address the feeling of a loss of fun and surprise experienced by many players using the new system. I personally do agree with those players. I miss that myself. 
It partially made me want to use the previous system.
How to address that?..
Well first I want to look at how the systems work.
From my observations the crafting system gives you 5 main goals you can try to accomplish. Those 5 goals are 5 rarity types. The crafting system allows numerous possible ways to achieve said goals. The system does not care what the players personal goals are. It always provides those 5 main goals. Crafting any rarity type that does not match a players personal goal will set the player back time, fragments, and credits.
From my observations the trade up system also had 5 main goals much like in the crafting system. The Trade Up system, however, only allowed one specific path to achieve each goal. The player had to go down the same path time and time again. The trade Up system also did not care about the players personal goals and still always provided the same goals.
Now here is the interesting thing I think…
Assuming the player will trade up everything to achieve their goal, I think the trade up system acts just like the crafting system. Any deviation from trading up to the players personal goal sets them back time, and credits.
These deviations occur every time a player decides to keep a card they made because it was a fun prize.
In my opinion, these deviations are the same logic wise as if a player decided to make a lower rarity card than what their personal goal is in the crafting system.
Basically I personally am find the two systems very similar minus the fun part of course. It’s these deviations that made the old system fun I think.
So now how to address the lack of apparent fun in crafting…
The main thing missing in crafting to me is the random surprises given to you from using the system itself. Honestly what comes to mind is to allow potential case drops when recycling or/and crafting. These cases can be rewarded as the player progresses to their individual goal. It kind of acts as a potential reward for players for using the system hopefully inspiring them to use it more and still keeps costs down… well in theory it should do all that.
It partially made me want to use the previous system.