Why would courage and energy need to be removed? That is specious logic.
They can remove the training trophy by itself. Like i have said multiple times it is the only trophy that gives direct improvement benefit to the entire team.
I have already stated why in my initial reply but since it seems you fail to understand let me spell it out for you. Courage and energy trophies over the course of time provide indirect benefits to training. Of course training trophies are the Holy Grail, they should be. That is not to say courage and energy do not have benefits though.
More courage means faster energy regen for dueling (+20 courage, -2 courage per duel). Duels = gold. Gold = stats.
More energy means more missions. Missions = experience + gold (and the occasional item which = even more gold). All this = stats.
Allow me to use myself as an example to illustrate: I am one of the oldest players in the game (currently 1259 days active as of the time of this post). I have never missed a single day of playing and typically use most if not all of my energy including refills. As a result, I also happen to be the strongest player on my server (and probably the other US servers as well). I routinely do 40+ duels every day. Currently sitting at 48262 won/48363 duels fought after 3.5+ years (38.41 duels per day average for the mathematically impaired).
Lets say my team had focused on more courage and energy and less training (ex: 2 courage, 3 energy).
+40 courage daily, 16 courage cost per duel
+60 energy daily
The optimal coin mission for me atm is 48k+ coin per 2 energy. So needless to say, more energy does yield better stats when focusing on purely coin missions. Now extrapolate using all this information i've given you to see how a player with the above benefits would have better stats than a player without.
Over time (weeks, months, years), said player would indeed be head and shoulders above someone who did not have such trophies. This is why you can't just arbitrarily remove all training trophy benefits retroactively because it would penalize players like myself who worked hard to get where we are today while simultaneously creating further imbalance by rewarding those who chose to focus on courage and energy and allowing them to keep said gains. Makes sense now?
Do you want to know what makes you and I so different? Our mindset.
I have only ever been on 3 teams over the course of 3.5 years. I used to get hammered in the beginning when I was an up-and-comer. I started more than a week after the server had launched so I had some catching up to do. I would typically have 30+ entries in my attack history every time I logged in. I realized early on that training trophies were the key to getting stronger and so I focused hard on doing pure coin missions to get my base stats up. That was the only way I could garner the attention of a strong team that actually had trophies.
I left my starter team at lvl 64 and joined a top 5 team that had 1 training trophy at that time. I stayed with that team from lvl 65 to 265. During that time I tried to convince my teammates that training trophies were the key to becoming stronger because unlike everyone else, my stat costs had gone through the roof by then and I knew the value of training units long before most did. They weren't convinced so I left to join another team.
From lvl 266 to my current lvl (422) I have been with the same team, surrounded by like minded individuals who have worked hard to become the best. Getting to the top is the easy part. Staying at the top is the real challenge. Time is the real enemy, boredom and stagnation for many due to lack of new content have caused quite a few to retire. So long story short... THAT is the difference between you and me. I never once complained about being the underdog, I never once came running to the forums asking for others to be nerfed, etc etc. I accepted that others were stronger than me so I worked harder to surpass them with what I was given instead of asking for a game-changing overhaul.
But the training trophy is the one that skews everything. No one else is out there hoarding energy trophies or courage trophies - and for good reason - because they have no direct benefit to skill points.
Maybe on your server that is the case but not on mine. A top 2 team has held on to many energy trophies for quite some time now. This has let them lvl up faster than most as well as been a huge boon to many of their members who find themselves consistently in the top 10 of the xp tournament week after week.